pax_global_header00006660000000000000000000000064133352421600014511gustar00rootroot0000000000000052 comment=45ab4d608ecfe5aad70e1f1d982a0f02501db09a bppsuite-2.4.1/000077500000000000000000000000001333524216000133505ustar00rootroot00000000000000bppsuite-2.4.1/AUTHORS.txt000066400000000000000000000027771333524216000152530ustar00rootroot00000000000000Julien Dutheil Céline Scornavacca Bastien Boussau Laurent Guéguen François Gindraud Contributed code to Bio++ was enabled thanks to the following institutions and resources: 2002 - 2006 Laboratoire GPIA - UMR CNRS 5171 Université Montpellier 2 (Eric Bazin, Khalid Belkhir, Guillaume Deuchst, Julien Dutheil, Sylvain Gaillard, Nicolas Galtier, Sylvain Glémin) 2005 - ISE-M UMR CNRS 5554 Université Montpellier 2 (Vincent Ranwez, Céline Scornavacca) 2006 - ISE-M UMR CNRS 5554 Université Montpellier 2 (Khalid Belkhir, Nicolas Galtier, Sylvain Glémin) 2006 - 2007 ISE-M UMR CNRS 5554 Université Montpellier 2 (Julien Dutheil) 2007 - 2010 Bioinformatics Research Center, University of Aarhus (Julien Dutheil). Funded by European research Area on Plant Genomics (ERA-PG) ARelatives. 2010 - ISE-M UMR CNRS 5554 Université Montpellier 2 (Julien Dutheil) 2007 - Genetics and Horticulture UMR INRA 1259 Angers-Nantes INRA Center (Sylvain Gaillard) 2008 - 2009 Laboratoire BBE - UMR CNRS 5558 Université Lyon 1 (Bastien Boussau) 2009 - 2010 Berkeley University (Bastien Boussau) 2010 - Laboratoire BBE - UMR CNRS 5558 Université Lyon 1 (Bastien Boussau) 2008 - Laboratoire BBE - UMR CNRS 5558 Université Lyon 1 (Laurent Guéguen) 2017 - 2018 Projet GrASP - LabEX Ecofect - Université de Lyon (François Gindraud) bppsuite-2.4.1/CMakeLists.txt000066400000000000000000000100431333524216000161060ustar00rootroot00000000000000# CMake script for Bio++ Program Suite # Authors: # Julien Dutheil # Francois Gindraud (2017) # Created: 22/08/2009 cmake_minimum_required (VERSION 2.8.11) project (bppsuite CXX) # Compile options SET (CMAKE_CXX_FLAGS "-std=c++11 -Wall -Weffc++ -Wshadow -Wconversion") IF(NOT CMAKE_BUILD_TYPE) SET(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE) ENDIF(NOT CMAKE_BUILD_TYPE) IF(NOT NO_DEP_CHECK) SET(NO_DEP_CHECK FALSE CACHE BOOL "Disable dependencies check for building distribution only." FORCE) ENDIF(NOT NO_DEP_CHECK) IF(NO_DEP_CHECK) MESSAGE(STATUS "Dependencies checking disabled. Only distribution can be built.") ELSE(NO_DEP_CHECK) #static linkage? IF(NOT BUILD_STATIC) SET(BUILD_STATIC FALSE CACHE BOOL "Enable static linkage." FORCE) ENDIF() IF(BUILD_STATIC) MESSAGE(STATUS "Static linkage requested.") SET(CMAKE_CXX_FLAGS "-static -static-libgcc ${CMAKE_CXX_FLAGS}") ENDIF() # Check compression program # COMPRESS_PROGRAM controls the choice of program # COMPRESS_EXT can be used to override the file extension if (NOT COMPRESS_PROGRAM) set (COMPRESS_PROGRAM gzip CACHE STRING "Set program for compressing documentation" FORCE) endif () find_program (COMPRESS_BIN NAMES ${COMPRESS_PROGRAM} DOC "${COMPRESS_PROGRAM} compression program") if (NOT COMPRESS_BIN) message (STATUS "${COMPRESS_PROGRAM} program not found, text doc will not be compressed") else () # Deduce COMPRESS_EXT for known compression programs if not set if (NOT COMPRESS_EXT) if (${COMPRESS_PROGRAM} STREQUAL "gzip") set (COMPRESS_EXT "gz") elseif (${COMPRESS_PROGRAM} STREQUAL "bzip2") set (COMPRESS_EXT "bz2") else () set (COMPRESS_EXT "${COMPRESS_PROGRAM}") # Default: program name (works for xz/lzma) endif () endif () # Generate command line args (always add -c to output compressed file to stdout) if (${COMPRESS_PROGRAM} STREQUAL "gzip") # -n for no timestamp in files (reproducible builds) # -9 for maximum compression (lintian error) set (COMPRESS_ARGS -c -n -9) else () set (COMPRESS_ARGS -c) endif () message (STATUS "Found ${COMPRESS_BIN} compression program, using file extension .${COMPRESS_EXT}") endif () # Find dependencies (add install directory to search) if (CMAKE_INSTALL_PREFIX) set (CMAKE_PREFIX_PATH "${CMAKE_INSTALL_PREFIX}" ${CMAKE_PREFIX_PATH}) endif (CMAKE_INSTALL_PREFIX) include (GNUInstallDirs) find_package (bpp-phyl 12.0.0 REQUIRED) find_package (bpp-popgen 8.0.0 REQUIRED) # Subdirectories add_subdirectory (bppSuite) add_subdirectory (doc) add_subdirectory (man) ENDIF(NO_DEP_CHECK) # Packager SET(CPACK_PACKAGE_NAME "bppsuite") SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team") SET(CPACK_PACKAGE_VERSION "2.4.1") SET(CPACK_PACKAGE_VERSION_MAJOR "2") SET(CPACK_PACKAGE_VERSION_MINOR "4") SET(CPACK_PACKAGE_VERSION_PATCH "1") SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Program Suite") SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt") SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt") SET(CPACK_RESOURCE_FILE_INSTALL "${CMAKE_SOURCE_DIR}/INSTALL.txt") SET(CPACK_SOURCE_GENERATOR "TGZ") # /!\ This assumes that an external build is used SET(CPACK_SOURCE_IGNORE_FILES "/build/" "/\\\\.git/" "/\\\\.gitignore" ${CPACK_SOURCE_IGNORE_FILES} ) SET(CPACK_SOURCE_PACKAGE_FILE_NAME "${CMAKE_PROJECT_NAME}-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}") SET(CPACK_DEBSOURCE_PACKAGE_FILE_NAME "${CMAKE_PROJECT_NAME}_${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}.orig") INCLUDE(CPack) #This adds the 'dist' target ADD_CUSTOM_TARGET(dist COMMAND ${CMAKE_MAKE_PROGRAM} package_source) IF(NOT NO_DEP_CHECK) IF (UNIX) #This creates rpm packages: ADD_CUSTOM_TARGET(rpm rpmbuild -ta ${CPACK_SOURCE_PACKAGE_FILE_NAME}.tar.gz) ADD_DEPENDENCIES(rpm dist info man) #ADD_DEPENDENCIES(info install) ENDIF(UNIX) ENDIF(NOT NO_DEP_CHECK) bppsuite-2.4.1/COPYING.txt000066400000000000000000000511531333524216000152260ustar00rootroot00000000000000CeCILL FREE SOFTWARE LICENSE AGREEMENT Notice This Agreement is a Free Software license agreement that is the result of discussions between its authors in order to ensure compliance with the two main principles guiding its drafting: * firstly, compliance with the principles governing the distribution of Free Software: access to source code, broad rights granted to users, * secondly, the election of a governing law, French law, with which it is conformant, both as regards the law of torts and intellectual property law, and the protection that it offers to both authors and holders of the economic rights over software. The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre]) license are: Commissariat à l'Energie Atomique - CEA, a public scientific, technical and industrial research establishment, having its principal place of business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris, France. Centre National de la Recherche Scientifique - CNRS, a public scientific and technological establishment, having its principal place of business at 3 rue Michel-Ange, 75794 Paris cedex 16, France. Institut National de Recherche en Informatique et en Automatique - INRIA, a public scientific and technological establishment, having its principal place of business at Domaine de Voluceau, Rocquencourt, BP 105, 78153 Le Chesnay cedex, France. Preamble The purpose of this Free Software license agreement is to grant users the right to modify and redistribute the software governed by this license within the framework of an open source distribution model. The exercising of these rights is conditional upon certain obligations for users so as to preserve this status for all subsequent redistributions. In consideration of access to the source code and the rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors only have limited liability. In this respect, the risks associated with loading, using, modifying and/or developing or reproducing the software by the user are brought to the user's attention, given its Free Software status, which may make it complicated to use, with the result that its use is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the suitability of the software as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions of security. This Agreement may be freely reproduced and published, provided it is not altered, and that no provisions are either added or removed herefrom. This Agreement may apply to any or all software for which the holder of the economic rights decides to submit the use thereof to its provisions. Article 1 - DEFINITIONS For the purpose of this Agreement, when the following expressions commence with a capital letter, they shall have the following meaning: Agreement: means this license agreement, and its possible subsequent versions and annexes. Software: means the software in its Object Code and/or Source Code form and, where applicable, its documentation, "as is" when the Licensee accepts the Agreement. 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The Licensee can include the Modified or unmodified Software in a code that is subject to the provisions of one of the versions of the GNU GPL, and distribute that entire code under the terms of the same version of the GNU GPL. Article 6 - INTELLECTUAL PROPERTY 6.1 OVER THE INITIAL SOFTWARE The Holder owns the economic rights over the Initial Software. Any or all use of the Initial Software is subject to compliance with the terms and conditions under which the Holder has elected to distribute its work and no one shall be entitled to modify the terms and conditions for the distribution of said Initial Software. The Holder undertakes that the Initial Software will remain ruled at least by this Agreement, for the duration set forth in Article 4.2. 6.2 OVER THE CONTRIBUTIONS The Licensee who develops a Contribution is the owner of the intellectual property rights over this Contribution as defined by applicable law. 6.3 OVER THE EXTERNAL MODULES The Licensee who develops an External Module is the owner of the intellectual property rights over this External Module as defined by applicable law and is free to choose the type of agreement that shall govern its distribution. 6.4 JOINT PROVISIONS The Licensee expressly undertakes: 1. not to remove, or modify, in any manner, the intellectual property notices attached to the Software; 2. to reproduce said notices, in an identical manner, in the copies of the Software modified or not. 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In particular the Parties expressly agree that any or all pecuniary or business loss (i.e. loss of data, loss of profits, operating loss, loss of customers or orders, opportunity cost, any disturbance to business activities) or any or all legal proceedings instituted against the Licensee by a third party, shall constitute consequential loss and shall not provide entitlement to any or all compensation from the Licensor. Article 9 - WARRANTY 9.1 The Licensee acknowledges that the scientific and technical state-of-the-art when the Software was distributed did not enable all possible uses to be tested and verified, nor for the presence of possible defects to be detected. In this respect, the Licensee's attention has been drawn to the risks associated with loading, using, modifying and/or developing and reproducing the Software which are reserved for experienced users. The Licensee shall be responsible for verifying, by any or all means, the suitability of the product for its requirements, its good working order, and for ensuring that it shall not cause damage to either persons or properties. 9.2 The Licensor hereby represents, in good faith, that it is entitled to grant all the rights over the Software (including in particular the rights set forth in Article 5). 9.3 The Licensee acknowledges that the Software is supplied "as is" by the Licensor without any other express or tacit warranty, other than that provided for in Article 9.2 and, in particular, without any warranty as to its commercial value, its secured, safe, innovative or relevant nature. Specifically, the Licensor does not warrant that the Software is free from any error, that it will operate without interruption, that it will be compatible with the Licensee's own equipment and software configuration, nor that it will meet the Licensee's requirements. 9.4 The Licensor does not either expressly or tacitly warrant that the Software does not infringe any third party intellectual property right relating to a patent, software or any other property right. Therefore, the Licensor disclaims any and all liability towards the Licensee arising out of any or all proceedings for infringement that may be instituted in respect of the use, modification and redistribution of the Software. Nevertheless, should such proceedings be instituted against the Licensee, the Licensor shall provide it with technical and legal assistance for its defense. 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No supplement or modification to the terms and conditions hereof shall be effective as between the Parties unless it is made in writing and signed by their duly authorized representatives. 11.4 In the event that one or more of the provisions hereof were to conflict with a current or future applicable act or legislative text, said act or legislative text shall prevail, and the Parties shall make the necessary amendments so as to comply with said act or legislative text. All other provisions shall remain effective. Similarly, invalidity of a provision of the Agreement, for any reason whatsoever, shall not cause the Agreement as a whole to be invalid. 11.5 LANGUAGE The Agreement is drafted in both French and English and both versions are deemed authentic. Article 12 - NEW VERSIONS OF THE AGREEMENT 12.1 Any person is authorized to duplicate and distribute copies of this Agreement. 12.2 So as to ensure coherence, the wording of this Agreement is protected and may only be modified by the authors of the License, who reserve the right to periodically publish updates or new versions of the Agreement, each with a separate number. These subsequent versions may address new issues encountered by Free Software. 12.3 Any Software distributed under a given version of the Agreement may only be subsequently distributed under the same version of the Agreement or a subsequent version, subject to the provisions of Article 5.3.4. Article 13 - GOVERNING LAW AND JURISDICTION 13.1 The Agreement is governed by French law. The Parties agree to endeavor to seek an amicable solution to any disagreements or disputes that may arise during the performance of the Agreement. 13.2 Failing an amicable solution within two (2) months as from their occurrence, and unless emergency proceedings are necessary, the disagreements or disputes shall be referred to the Paris Courts having jurisdiction, by the more diligent Party. Version 2.0 dated 2006-09-05. bppsuite-2.4.1/ChangeLog000066400000000000000000000150021333524216000151200ustar00rootroot0000000000000019/03/18 -*- Version 2.4.0 -*- 19/02/18 Julien Dutheil * Bug fixed in bppPopStats: dN and dS were inverted! 10/12/17 -*- Version 2.3.2 -*- 06/11/17 Julien Dutheil * Added estimation of kappa to bppPopStats + bugs fixed 06/06/17 -*- Version 2.3.1 -*- 10/05/17 -*- Version 2.3.0 -*- 21/12/16 Julien Dutheil * BppPhySamp migrated to its own package. 17/12/16 Julien Dutheil * Improved bppPopStats, outgroup analyses, MK table and output to file. 06/10/16 Julien Dutheil * bppSeqGen now takes Hudson's MS ARG files as input. * new input.tree.scale option to adjust branch lengths. 22/05/16 Julien Dutheil * bpppopstats now computes codon statistics per site (e.g. PiN, PiS) * Added example for bpppopstats. 29/06/15 Julien Dutheil * New program bppPopStats 28/01/15 Julien Dutheil * PhySamp now outputs the correct tree! 25/11/14 Julien Dutheil * bppalnscore output contiguous segments in mase selection. * bppalnscore site selection works with codon alphabets. 24/11/14 Julien Dutheil * bppSeqMan can now read alignments and perform site selection priori to any analysis. 28/09/14 -*- Version 2.2.0 -*- 16/09/14 Julien Dutheil * bppSeqGen supports generic characters as ancestral states in info file (bug #87). 12/08/14 Julien Dutheil * bppSeqGen supports simulation under Markov-Modulated models. 06/06/14 Julien Dutheil * bppPhySamp now ouput trees as well. 17/04/14 Julien Dutheil * bppSeqMan: Translate uses global genetic_code argument instead of local 'code' argument. * All programs use the --seed argument to set random seed for reproduceable results. 08/03/13 -*- Version 0.8.0 -*- 22/01/13 Julien Dutheil * Compiles with -Wconversion 14/01/13 Mathieu Groussin * Added COaLA model for proteins in bppML and bppSeqGen. 23/11/12 Laurent Guéguen * New bppMixedLikelihood program 08/02/12 -*- Version 0.7.0 -*- 21/12/11 Julien Dutheil * New bppAlnScore program * Improved bppSeqMan: protein translation now works + more stop codons removal options. 17/06/11 Julien Dutheil * Improved bppancestor, also allows to compute frequencies for leaves. 11/06/11 -*- Version 0.6.2 -*- * Small bug fixed + new packages. 03/06/10 -*- Version 0.6.0 -*- * Compatibility with Bio++ 2.0.0. 03/06/10 Julien Dutheil * New method in bppPhySamp + new, faster, implementation. 25/03/10 -*- Version 0.5.0 -*- 22/08/09 Julien Dutheil * Added CMake configuration files, with twick for building the manual (assumes texinfo is installed). 22/07/09 Julien Dutheil * Added program bppTreeDraw. 30/06/09 Julien Dutheil * BppAncestor: now output expected ancestral states frequencies. * BppAncestor: new method to compute EB estimates of ancestral states frequencies. 10/06/09 -*- Version 0.4.0 -*- 22/05/09 Julien Dutheil * Keyval syntax for sequence format description. * Documentation and example update. * SeqMan now uses the SequenceApplicationTools method. 15/05/09 Julien Dutheil * Compatibility update with the libs, new keyval syntax for model specification. * Documentation up to date. 02/02/09 Julien Dutheil * bppConsense now outputs the number of leaves of the input tree. * New progress bar in bppConsense. 08/01/09 Julien Dutheil * Added texinfo documentation. * More bootstrap options in BppDist (the same as in BppML). 25/09/08 -*- Version 0.3.1 -*- 07/12/08 Bastien Boussau & Julien Dutheil * Bug removed in non-homogeneous models with covarions. 09/10/08 Julien Dutheil * New action 'invert' in bppSeqMan. 25/09/08 -*- Version 0.3.0 -*- 20/09/08 Julien Dutheil * New program bppAncestor to reconstruct acestral states and rates. * New +F models from PhylLib. 02/07/08 Laurent Guegen * Bug fixed in bppML: frequencies can be computed from the data with non-homogeneous models. 19/06/08 Julien Dutheil * Shell variables are now 'global' in option files. 24/04/08 -*- Version 0.2.3 -*- * This version requires the CVS version of Bio++ to be built. 03/03/08 Julien Dutheil * Bug fixed in keep_complete method of BppSeqMan. 27/03/08 Julien Dutheil * Bug fixed when printing parameters of non-homogeneous models in bppML. 22/01/08 -*- Version 0.2.2 -*- 28/02/08 Celine Scronavacca * Bug fixed in ReRoot. 22/01/08 -*- Version 0.2.1 -*- 06/02/08 Celine Scornavacca * Bug fixed in ReRoot + correction of version number in bppSeqGen. 22/01/08 -*- Version 0.2.0 -*- 13/01/08 Julien Dutheil * More options in bppml: possibility to chose between simple and double recursion and data compression method. * Simple recursion method improved. 11/01/08 Julien Dutheil * Compatibility update * bppML now output more handy parameter values. 31/12/07 Julien Dutheil * New program Phylo Sampler. 07/11/07 Julien Dutheil * Compatibility update with Bio++ cvs. * Bug fixed in BppSeqGen. * BppSeqGen can now simulate datas from a set of trees (ancestral recombination graph). 25/10/07 Julien Dutheil * Several bug fixed in BppML and BppSeqGen with non-homogeneous models. * Examples updated + new example option files for non-homogeneous models. 05/10/07 Bastien Boussau & Julien Dutheil * Non-homogenous sequence simulation in BppSeqGen. * Model options in files have changed to suit the non-homogeneous case. The covarion option now is fully part of the model options, following the new syntax 'model=modelname+covarionname', eg 'T92+G2001'. 03/10/07 Julien Dutheil * New program Bio++ Sequence Manipulator 21/09/07 Julien Dutheil * Bug fixed in BppDist: branch length are indeed not estimated when parameters to ignore contains "BrLen". * Stop condition when using iterations is now based on topological distance instead of likelihood comparisons (phyllib). * New option optimization.topology_nni.method = [fast|better|phyml] 17/06/07 -*- Version 0.1.0 -*- 16/07/06 Julien Dutheil * New option bootstrap.verbose for bppML. * Bug fixed in bootstrap computation. 06/06/06 Julien Dutheil * New program bppConsense. 05/05/07 Julien Dutheil * First alpha release of bppsuite. -*- Old bppML ChangeLog -*- 23/04/07 Julien Dutheil - Optimization with a global clock. - Possibility to set branch lengths before ML optimization, with different methods. 25/01/07 Julien Dutheil * Version 1.0.0 - Topology search for ML - User input tree may be random, nj or bionj. - Possibility to make a parsimony search before ML estimation. 28/08/06 Julien Dutheil * Version 0.2.0 - Covarion models - New optimization methods. 30/05/06 Julien Dutheil * option --enable-static in configure. 19/04/06 Julien Dutheil * Version 0.1.2 * Update for library compatibility * Check for 0 branch lengths leading to 0 likelihood before optimization. * New output.estimates options to get the final parameter values after optimization. bppsuite-2.4.1/Examples/000077500000000000000000000000001333524216000151265ustar00rootroot00000000000000bppsuite-2.4.1/Examples/AlignmentScoring/000077500000000000000000000000001333524216000203715ustar00rootroot00000000000000bppsuite-2.4.1/Examples/AlignmentScoring/AlnScores.bpp000066400000000000000000000005371333524216000227720ustar00rootroot00000000000000DATA=HIV1_REF_2010_gag input.sequence.file.test = ../Data/$(DATA)_DNA.fasta input.sequence.format.test = Fasta input.sequence.file.ref = ../Data/$(DATA)_macse_DNA.fasta input.sequence.format.ref = Fasta score.word_size = 3 score.phase = ATG output.scores = $(DATA).scores.txt output.mase = $(DATA).filter.mase output.sps_thresholds = 0.8 bppsuite-2.4.1/Examples/ConsensusTree/000077500000000000000000000000001333524216000177265ustar00rootroot00000000000000bppsuite-2.4.1/Examples/ConsensusTree/Consense.bpp000066400000000000000000000005641333524216000222130ustar00rootroot00000000000000input.trees.file = ../Data/treeList.dnd input.trees.format = Newick # [input|consensus] tree = Input input.tree.file = boot.nx #../Data/tree.dnd input.tree.format = Nexus #Newick # Alternatively: # tree = Consensus(threshold=0.5) # 0 = fully resolved # 0.5 = majority rule # 1 = strict # or any intermediate value... output.tree.file = boot.nx output.tree.format = Nexus bppsuite-2.4.1/Examples/Data/000077500000000000000000000000001333524216000157775ustar00rootroot00000000000000bppsuite-2.4.1/Examples/Data/HIV1_REF_2010_gag_DNA.fasta000066400000000000000000002366641333524216000222050ustar00rootroot00000000000000>Ref.A1.AU.03.PS1044_Day0.DQ676872 ATGGGTGCGAGAGCGTCAATATTAAGCGGGGGAAGATTAGATGCATGGGA GAAAATTCGGCTAAGGCCAGGGGGAAAGAAAAAATATAGACTAAAACATC TAGTATGGGCAAGCAGGGAGCTGGAGAGATTCGCACTTAAYCCTRGCCTT TTAGAATCAGCAGAAGGATGTCAACAAATAATGGAACAGTTACAACCAGC TCTYAAGACAGGAWCAGAAGAAATTAAATCATTATTTAATACAGTAGCAA CCCTCTATTGTGTACATCAAAGGATAGATGTAAAAGACACCAAGGAAGCT YTAGATAAAATAGAGGAAATAAAA------------AAT----------- ----------AAG---------------AGCAAG------CAAAGG---- -----------------------------ACTCAACAGGCAGCAGCT--- ------------------------------GACACAGGA----------- -------------------------------------------------- -----------------------------AACAGCGGCAAG--------- ---------GTCAGCCAAAATTACCCTATAGTGCAAAATGCACAGGGGCA AATGATACAYCAAAACTTGTCACCTAGAACTTTAAATGCATGGGTAAAAG TAATAGAA---GAAAAGGCTTTTAGTCCAGAAGTGATACCCATGTTCTCA GCATTATCAGAAGGAGCCACCCCACAAGATTTAAATGTAATGCTGAACAT AGTGGGGGGACACCAGGCAGCTATGCAAATGTTAAAAGACACCATCAATG AAGAAGCTGCAGAATGGGACAGGTTACATCCAGTACATGCAGGGCCTATT CCACCAGGCCAGATAAGAGAACCAAGGGGAAGTGACATAGCAGGAGCTAC TAGTACCCCTCAAGAACAATTACAATGGATGACA---------GGCAACC CACCTATC---CCAGTGGGAGACATCTATAAAAGATGGATAATCCTGGGA TTAAATAAAATAGTAAGAATGTATAGCCCTACTAGCATTTTGGATATAAG ACAAGGGCCAAAAGAATCCTTCAGAGACTATGTAGATAGGTTCTTTAAAG CTCTTAGAGCTGAGCAAGCTACACAGGAGGTAAAAAGTTGGATGACAGAG ACATTACTGGTC---CAAAATGCAAATCCAGATTGTAAGTCCATTCTAAA AGCATTAGGATCAGGAGCTACATTAGAAGAAATGATGACAGCATGCCAGG GAGTGGGAGGACCCAGCCATAAGGCAAGGGTTTTGGCTGAAGCAATG--- ---------AGTCAAGCACAA------------------------CAAAC AAGCATAATGATGCAGAGA---GGCAAC---TTTAGGGGCGGCCAGAAA- --AGG---ATTAAGTGTTTTAACTGTGGCAAAGAAGGACACCTAGCCAGA AATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGGAAGGAGGG ACACCAAATGAAAGACTGCACT---------GAA---AGACAGGCTAATT TTTTAGGGAAAATTTGG---CCT---TCCAGCAAG---------GGG--- AGGCCAGGAAATTTCCCTCAGAGC-------------------------- ----AGACCA------GAGCCAACAGCC---------------------- -----------------------------CCACCAGCG---GAGCTCTTT GGGATGGGG---------------GAAGAGATA---ACCTCCCCT----- -------------------CCGAAGCAGGAGCAG---------------- --------AAGGACAAG---------------------GAACAGGTC--- ---CCACCC---TTA---GTTTCCCTCAAATCACTCTTTGGCAACGACCC ATCGTCACAGTAA >Ref.A1.RW.92.92RW008.AB253421 ATGGGTGCGAGAGCGTCAGTATTAAGTGGGGGAAAATTAGATGCATGGGA AAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAGAATGAAACATC TAGTATGGGCAAGCAGGGAGCTGGAAAGATTTGCACTTAACCCTGGCCTT TTAGAAACAACAGAAGGATGTCAAAAAATAATAGAACAGTTACAACCATC TGTCAAGACAGGAACAGAAGAACTTAAATCATTATTTAATACAGTAGCAA CCCTCTATTGCGTACATCAACGGATAGATGTAAAAGACACCAAGGAAGCC CTAGATAAAATAGAGGAAATGCAA------------AAT----------- ----------AAG---------------AGCAAG------CAAAAG---- -----------------------------ACACAACAGGCAGCAGCT--- ------------------------------GACATAGGA----------- -------------------------------------------------- -----------------------------AATAGCAGCAAG--------- ---------GTCAGCCAAAATTACCCTATAGTGCAAAATGCACAAGGGCA AATGATATATCAGTCCATGTCACCTAGGACTTTGAATGCATGGGTGAAAG TAATAGAA---GAAAAGGGTTTCAACCCAGAAGTAATACCCATGTTCTCA GCATTATCAGAAGGAGCCACCCCACAAGATTTAAATATGATGCTAAACAT AGTGGGGGGACATCAGGCAGCTATGCAAATGTTAAAAGATACCATCAATG AGGAAGCTGCAGACTGGGACAGGTTACATCCAGTACAGGCAGGGCCTATT CCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTAC TAGTACCCCTCAAGAACAAATAGGATGGATGACA---------AGCAACC CACCTATC---CCAGTGGGAGACATCTATAAAAGATGGATAATCCTGGGA TTAAATAAAATAGTAAGAATGTATAGCCCTGTTAGCATTTTGGATGTAAA ACAAGGGCCAAAAGAACCCTTTAGAGATTATGTAGATAGGTTCTTTAAAA TTCTCAGAGCTGAACAAGCTACACAGGATGTAAAACATTGGATGACAGAA ACATTGCTGATC---CAAAATGCAAATCCAGATTGTAAGTCCATTTTAAG AGCATTAGGAACAGGGGCTACATTAGAAGAAATGATGACAGCATGTCAGG GAGTGGGAGGACCCAGCCATAAAGCAAGGGTTTTAGCTGAGGCAATG--- ---------AGTCAAGTACAA------------------------CATCC AAACATAATGATGCAGAGA---GGCAAT---TTTAGGGGC---CAGAAA- --AGG---ATTAAGTGCTTCAACTGTGGCAAAGAAGGACACCTAGCCAGA AATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAGGG ACACCAAATGAAAGACTGCACT---------GAA---AGACAGGCTAATT TTTTAGGGAAAATTTGG---CCT---TCCAGCAAG---------GGG--- AGGCCAGGAAATTTTCCTCAGAGC-------------------------- ----AGACCG------GAGCCATCAGCC---------------------- -----------------------------CCACCAGCA---GAGATCTTT GGGATAGGG---------------GAAGAGATA---GCCTCCCCT----- -------------------CCGAAGCAGGAGCAG---------------- --------AAAGACAGG---------------------GAACCGGCC--- ---CAACCT---TTA---GTTTCCCTCAAATCACTCTTTGGCAACGACCC CTTGTCACAGTAA >Ref.A1.UG.92.92UG037.AB253429 ATGGGTGCGAGAGCGTCAGTATTAAGTGGGGGAAAATTAGATGCATGGGA GAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAGATTAAAACATC TAGTATGGGCAAGCAGGGAGCTGGAAAGATTTGCACTTAACCCTAGCCTT TTAGAAACAACAGAAGGATGTCAACAAATAATGGAACAATTACAATCAGC TCTCAGAACAGGAACAGAAGAACTTAGATCATTATATAATACAGTAGCAA CCCTCTATTGCGTACATCAACGGATAGAGGTAAAAGACACCAAGGAAGCT CTAGATAAAATAGAGGAGATACAA------------AAG----------- ----------AAA---------------AGCAAG------CAAAAG---- -----------------------------ACACAGCAGGCAGCAGCT--- ------------------------------GACACAGGA----------- -------------------------------------------------- -----------------------------AGTAGCAGCAAG--------- ---------GTCAGCCAAAATTACCCTATAGTGCAAAATGCACAAGGGCA AATGATCCACCAGTCCTTGTCACCTAGGACTTTGAATGCATGGGTGAAAG TAATAGAA---GAAAAGGCTTTCAGCCCAGAAGTAATACCCATGTTCTCA GCATTATCAGAAGGAGCCACCCCACAAGATTTGAATATGATGCTGAACAT AGTGGGGGGACACCAGGCAGCTATGCAAATGTTAAAAGATACCATCAATG AGGAAGCTGCAGAATGGGACAGGCTACATCCAGTACATGCAGGGCCTGTT GCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGATATAGCAGGAACTAC TAGTACCCCTCAAGAACAAATAGCATGGATGACA---------GGCAACC CACCTATC---CCAGTGGGAGACATCTATAAAAGATGGATAATCCTGGGA TTAAATAAAATAGTAAGAATGTATAGCCCTGTTAGCATTTTAGATATAAA ACAAGGGCCAAAAGAACCCTTCAGAGACTATGTAGATAGGTTTTTTAAAA CTCTCAGAGCTGAGCAAGCTACACAGGAGGTAAAAGGTTGGATGACAGAA ACATTACTGATC---CAAAATGCAAATCCAGATTGTAAATCCATCCTAAG AGCATTAGGAGCAGGGGCTACATTAGAAGAAATGATGACAGCATGCCAGG GAGTGGGAGGACCCGGCCATAAAGCAAGAGTTTTGGCTGAGGCAATG--- ---------AGTCAAGTACAA------------------------CATAC AAACATAATGATGCAGAGA---GGCAAT---TTTAAGGGC---CAGAAA- --AGG---ATTAAGTGTTTCAACTGTGGCAAAGAAGGACATCTAGCCAAA AATTGCAGGGCTCCTAGAAAAAAGGGCTGTTGGAAATGTGGAAGGGAAGG GCACCAAATGAAGGACTGCACT---------GAG---AGACAGGCTAATT TTTTAGGGAAAATCTGG---CCT---TCCAGCAAA---------GGG--- AGGCCAGGAAATTTTCCTCAGAGC-------------------------- ----AGACCA------GAACCAACAGCC---------------------- -----------------------------CCACCAGCAGCAGAGATCTTT GGGATGAGG---------------GAAGAGATA---GTCTCCCCT----- -------------------CCGAAGCAGGAGCAG---------------- --------AACGACAGG---------------------GACCAGAAC--- ---CCACCT---TCA---GTTTCCCTCAAATCACTCTTTGGCAACGACCT CTTGTCACAGTAA >Ref.A2.CD.97.97CDKTB48.AF286238 ATGGGTGCGAGAGCGTCAGTATTGAGCGGCGGAAAATTAGAAGCTTGGGA GAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAGACTGAAACATT TAGTATGGGCAAGCAGGGAGCTGGAAAAATTCTCAATCAACCCCAGCCTT TTAGAAACAGAAACAGGATGTAGACGAATATTTGGGCAATTACAACCAGC TCTCGAGACAGGAACAGAAGAACTTAGATCATTATATAATACAATAGCAG TCCTCTACTTTGTTCATCAAAAGATAGAGGTAAAAGACACCAAGGAAGCT CTAGATAAAATAGAGGAAGAACAA------------AAC----------- ----------AAA---------------TGCAAG------CAGAAG---- -----------------------------ACACAGCAGGCAGCAGCT--- ------------------------------GACACAGGA----------- -------------------------------------------------- -----------------------------AGCAGCAGCAGTCAAAATTAC AGAGGTAGCAGCAGTCAAAATTACCCTATAGTGCAAAATGCACAAGGGCA AATGGTACACCAGGCCGTGTCACCTAGGACTTTGAATGCATGGGTCAAAG TAGTTGAA---GAGAAGGCTTTTAGCCCAGAAGTAATACCCATGTTTACA GCATTATCAGAAGGAGCCACCCCACAAGACTTAAATACTATGCTAAACAC AGTGGGGGGACATCAAGCAGCTATGCAAATGTTAAAAGATACCATCAATG AGGAAGCTGCAGAATGGGACAGGTTACATCCAGTACAGGCAGGGCCTATT CCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCGGGAGCTAC TAGTAACCTTCAGGAACAAATAGGATGGATGACC---------AGCAACC CACCTATT---CCAGTGGGAGAAATCTATAAAAGATGGATAATCCTGGGA TTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAA ACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGATAGGTTCTTTAAAA CTCTCAGAGCTGAGCAAGCTACACAGGAGGTAAAAAATTGGATGACAGAC ACCTTGCTGGTC---CAAAATGCAAACCCAGATTGTAAATCCATCTTGAG GGCATTAGGACCAGGGGCTACATTAGAAGAAATGATGACAGCATGTCAGG GAGTGGGAGGACCCGGCCATAAAGCAAGGGTTTTAGCTGAAGCAATG--- ---------AGCCAAGTACAA------------------------AATAC AAACATAATGATACAGAGA---GGCAAT---TTTAAGGGT---CAAAAA- --AGA---ATTAAGTGTTTCAACTGTGGCAAGGAAGGACACCTAGCTAGA AATTGCAGGGCCCCTAGGAAAAAGGGCTGCTGGAAATGTGGGAAGGAAGG ACATCAAATGAAAGACTGCACT---------GAG---AGACAGGCTAATT TTTTAGGGAAAATTTGG---CCT---TCCAACAAA---------GGG--- AGGCCAGGGAATTTTCCTCAGAGC-------------------------- ----AGGACA------GAGCCAACAGCC---------------------- -----------------------------CCACCAATG------------ ------GAG---------------GAAGAGATA---ACCTCCTCG----- -------------------CTGAAGCAGGAG------------------- -----------AACAGG---------------------GAGCCGTCC--- ---ACCCCT---GCA---ATTTCCCTCAAATCACTCTTTGGCAACGACCT CTTGTCACAGTGA >Ref.A2.CM.01.01CM_1445MV.GU201516 ------GCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCTTGGGA GAAAATTCGGTTAAGGCCAGGGGGAAGGAAAAAATATAGAATGAAACATT TAGTATGGGCAAGCAGGGAGCTGGAAAAATACTCAATCAACCCTGGTCTT TTAGAAACATCGGAAGGATGTAAACAAATAATAAGGCAGTTACATTCAGC TCTCCCAGTAGGAACAGAAGAACTTAAATCACTATATAATACAATAGCAG TCCTCTACTATGTACATCAAAAAATAGAGGTAAAAGACACCAAGGAAGCC CTAGATAAATTAGAGGAGGAGCAA------------AAC----------- ----------AAA---------------TACAAG------CAGAAG---- -----------------------------ACACAGCAGGCAGCAGCT--- ------------------------------GCCACAGGA----------- -------------------------------------------------- -----------------------------AATAGCAGC------------ ------------AGTCAGAATTATCCCATAGTGCAAAATGCACAAGGGCA AATGGTGCACCAGGCCATATCGCCTAGGACTTTGAATGCATGGGTCAAAG TAGTAGAA---GAAAAAGCTTTCAGCCCAGAAGTAATACCCATGTTTTCA GCATTATCAGAAGGAGCCACCCCACAAGATTTAAATACTATGCTAAACAC AGTGGGGGGACATCAAGCAGCTATGCAAATGTTAAAGGATACCATCAATG AGGAAGCTGCAGAATGGGACAGGGTACATCCAGTACATGCAGGGCCTATT CCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTAC TAGTACCCTTCAGGAACAAATAGGATGGATGACC---------AGCAACC CACCTATC---CCAGTGGGAGAAATCTATAAAAGATGGATAATCCTGGGA TTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAG ACAAGGGCCCAAAGAACCCTTTAGAGACTATGTAGATAGGTTCTTTAAAA CTCTCAGAGCTGAACAAGCTACACAGGATGTAAAAAATTGGATGACAGAC ACCTTGCTGGTC---CAAAATGCGAACCCAGATTGTAAAACTATCCTGAG AGCGTTAGGACCAGCGGCTACATTAGAAGAAATGATGACAGCATGTCAGG GAGTGGGAGGACCCGGCCATAAAGCAAGGGTCTTGGCTGAAGCAATG--- ---------AGCCAAATACACAGTACA------------------AATCA AAATGTAATGATGCAGAGA---GGCAAT---TTTAGAGGT---CCAAAA- --AGA---ATTAAGTGTTTCAACTGTGGCAAGGAAGGACACCTAGCCAGA AATTGCAGGGCCCCTAGGAAAAAGGGTTGCTGGAAATGTGGGAAGGAAGG ACATCAAATGAAAGATTGCACT---------GAG---AGACAGGCTAATT TTTTAGGGAAAATCTGG---CCT---CCCAACAAA---------GGG--- AGGCCAGGAAACTTTCCCCAGAGC-------------------------- ----AGAACA------GAGCCAACAGCC---------------------- -----------------------------CCGCCAGCA---GAGAACGTT GGAATGGGG---------------GAAGAGATA---GCTTCCTCG----- -------------------TCGAAGCAGGAACTG---------------- --------AGAAACAGG---------------------GAACAACAC--- ---ACTCCT---ACA---ATTTCCCTCAGATCACTCTTTGGCAACGACCC CTTGTCACAGTAA >Ref.A2.CY.94.94CY017_41.AF286237 ATGGGTGCGAGAGCGTCAATATTAAGCGGGGGAAAATTAGATGCTTGGGA GAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAGACTGAAACATT TGGTATGGGCAAGCAGGGAGCTGGAGAAATTCTCAATTAACCCTGGCCTT TTAGAAACACCAGAGGGATGTAGACAAATAATAAGGCAGTTACAACCAGC TCTCCAAACAGGAACAGAAGAACTTAAATCATTATATAATACAGTAGTAG TCCTCTACTGGGTACATCAAAGGGTAGATGTAAAAGACACCAAGGAAGCT CTAGATAAAATAGAGGAAGAACAA------------AAC----------- ----------AAG---------------------------CAGAAA---- -----------------------------ACACAGCATGCAGCAGCT--- ------------------------------GACACAGGG----------- -------------------------------------------------- -----------------------------AACAGCAGC------------ ------------AGTCAAAATTATCCCATAGTGCAAAATGCACAAGGGCA AATGGTACACCAGGCTATATCACCTAGGACGTTGAATGCCTGGGTCAAAG TAGTAGAA---GAAAAGGCTTTCAGCCCAGAAGTAATACCTATGTTTACA GCATTATCAGAAGGAGCCACCCCACAAGACTTAAATACTATGCTAAACAC AGTGGGGGGACATCAAGCAGCTATGCAAATGTTAAAAGATACCATCAATG AGGAAGCTGCAGAATGGGACAGGGTACATCCAGTACATGCAGGGCCTATT CCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTAC TAGTACCCTTCAGGAACAAATAGGTTGGATGACC---------AGCGATC CACCCATC---CCAGTGGGAGAAATTTATAAAAGATGGATAATCCTGGGA TTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAG ACAAGGGCCAAAAGAACCCTTTAGAGATTATGTGGATAGGTTCTTTAAAA CTCTAAGAGCTGAGCAAGCCACACAGGAGGTAAAAAACTGGATGACGGAC ACCTTGCTGGTC---CAAAATGCGAACCCAGATTGTAGATCCATCTTGAG AGCATTAGGACCAGGGGCCTCATTAGAAGAAATGATGACAGCATGTCAGG GAGTGGGAGGACCCAGCCATAAAGCAAGGGTTTTGGCTGAAGCAATG--- ---------AGCCATGTACAAAGTACA------------------AATAC AAACATAATGATGCAGAGA---GGCAAT---TTTAGGGGT---CAAAAA- --AGA---ATTAAGTGTTTCAACTGTGGCAAGGAAGGACACCTAGCCAGA AATTGCAGGGCCCCTAGGAAAAAGGGCTGCTGGAAATGTGGAAAGGAAGG ACATCAAATGAAAGATTGCACT---------GAG---AGACAGGCTAATT TTTTAGGGAAAATTTGG---CCT---TCCAACAAA---------GGG--- AGGCCAGGAAATTTTCCTCAGAGC-------------------------- ----AGAACA------GAGCCAACAGCC---------------------- -----------------------------CCACCAGCA---GAGAACTTG AGAATGGGG---------------GAAGAGATA---ACCTCCTCC----- -------------------CTGAAGCAGGAACTG---------------- --------GAGACCAGG---------------------GAACCATAC--- ---AATCCT---GCA---ATTTCCCTCAAATCACTCTTTGGCAACGACCC CTTGTTACAGTAA >Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGA AAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATA TAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTG TTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATC CCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAA CCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCT TTAGACAAGATAGAGGAAGAGCAA------------AAC----------- ----------AAA---------------AGTAAG------AAAAAA---- -----------------------------GCACAGCAAGCAGCAGCT--- ------------------------------GACACAGGA----------- -------------------------------------------------- -----------------------------CACAGCAATCAG--------- ---------GTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCA AATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAG TAGTAGAA---GAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCA GCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACAC AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATG AGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATT GCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTAC TAGTACCCTTCAGGAACAAATAGGATGGATGACA---------AATAATC CACCTATC---CCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGA TTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAG ACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAA CTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAA ACCTTGTTGGTC---CAAAATGCGAACCCAGATTGTAAGACTATTTTAAA AGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGG GAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATG--- ---------AGCCAAGTAACAAAT---------------------TCAGC TACCATAATGATGCAGAGA---GGCAAT---TTTAGGAAC---CAAAGA- --AAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGA AATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGG ACACCAAATGAAAGATTGTACT---------GAG---AGACAGGCTAATT TTTTAGGGAAGATCTGG---CCT---TCCTACAAG---------GGA--- AGGCCAGGGAATTTTCTTCAGAGC-------------------------- ----AGACCA------GAGCCAACAGCC---------------------- -----------------------------CCACCAGAA---GAGAGCTTC AGGTCTGGG---------------GTAGAGACAACAACTCCCCCT----- -------------------CAGAAGCAGGAGCCG---------------- --------ATAGACAAG---------------------GAACTGTAT--- ------CCT---TTA---ACTTCCCTCAGGTCACTCTTTGGCAACGACCC CTCGTCACAATAA >Ref.B.NL.00.671_00T36.AY423387 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATAGATGGGA AAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAGATATAAATTAAAACATA TAGTATGGGCAAGCAGAGAGCTAGAACGATTCGCAGTTAATCCTGGCCTT TTAGAGACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCAGC CCTTCAGACAGGATCAGAAGAACTTAAATCATTATTTAATACAGTAGCAA CCCTCTATTGTGTGCATGCAAGGATAGAGGTAAAAGACACCAAGGAAGCT TTAGAAAAAATAGAGGAAGAACAA------------AAC----------- ----------AAA---------------AGTAAG------AAACGG---- --------------GCACAGCAA------GCACAGCAAGCAGAAGCT--- ------------------------------GACGCAGGA----------- -------------------------------------------------- -----------------------------AAAAACAACCCG--------- ---------GTCAGCCAGAATTACCCTATAGTGCAGAATCTCCAAGGGCA AATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAG TAGTAGAA---GAGAAGGCCTTCAGCCCAGAAGTAATACCCATGTTTTCA GCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACAC AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATG AGGAAGCTGCAGAATGGGATAGATTGCATCCAGTGCATGCCGGGCCTATT GCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTAC TAGTACCCTTCAGGAACAAATAGGATGGATGACA---------AATAATC CACCTATC---CCAGTAGGAGAAATATATAAGAGATGGATAATCCTGGGA TTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAA ACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGATCGGTTCTATAAAA CTTTAAGAGCTGAGCAAGCCTCACAGGAAGTAAAAAATTGGATGACAGAA ACCTTGTTGGTC---CAAAATTCGAACCCAGATTGTAAAACTATTTTAAA AGCATTGGGACCAGCAGCTACACTAGAAGAAATGATGACCGCATGTCAGG GAGTAGGGGGACCCGGCCATAAAGCGAGAGTTTTGGCTGAGGCAATG--- ---------AGCCAAGTAACAAGT---------------------GCACC TGCCATAATGATGCAGAGA---GGCAAT---CATAGAAAC---CAAAGA- --AGGACTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACATAGCCAGA AATTGCAGGGCCCCTAGNAAAAAGGGCTGTTGGAAATGTGNAAAGNAAGG ACACCAAATGAAAGATTGTACT---------NAG---AGACAGGCTANTT TTTTAGGGAAGATTTGG---CCT---TCCCACAAG---------GGG--- AGGCCAGGGAATTTTCTTCAGAGC-------------------------- ----AGACCA------GAGCCAACAGCC----------------CCTTCT CAGAGCAGACCAGAGCCAAC---AGCC--CCACCAGAA---GAGAGCTTC AGGTTTGGG---------------GAAGAGACAACAACTCCCTCT----- -------------------CAGAGGCAGGAGCCA---------------- --------ACAGACAAG---------------------GAACTGTAT--- ------CCT---TTA---GCTTCCCTCAAATCACTCTTTGGCAGCGACCC ATAGTCACAATAA >Ref.B.TH.90.BK132.AY173951 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGACAATTAGATAGATGGGA GAAAATTCGGTTACGGCCAGGGGGAAAGAAAAAATATAGATTAAAACATA TAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTA TTGGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCAAG CCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAATAGCAG TCCTCTATTGTGTACATCAAAAGATAGAGGTAAAAGACACCAAGGAAGCT TTAGAGAAGATAGAGGAAGAACAA------------AAC----------- ----------AAA---------------AGTAAG------AAAAAG---- -----------------------------GCACAGCAAGCAGCAGCT--- ------------------------------AACACAGAA----------- -------------------------------------------------- -----------------------------AACAGCAGCCAG--------- ---------GTTAGCCAAAATTACCCTATAGTGCAAAATATGCAGGGGCA AATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAG TAGTAGAA---GAAAAGGCTTTCAGCCCAGAAGTAATACCCATGTTTTCA GCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACAC AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATG AGGAAGCTGCAGAATGGGATAGATTGCATCCAGTGCATGCAGGGCCTATT GCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTAC TAGTACCCTTCAGGAACAAATAGGATGGATGACA---------CATAATC CACCTATC---CCAGTGGGAGAAATTTACAAAAGATGGATAATCCTGGGA TTAAATAAAATAGTAAGGATGTATAGCCCTACCAGCATTTTGGACATAAG ACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAGA CTCTAAGAGCCGAGCAAGCCTCACAGGAGGTAAAAAATTGGATGACAGAA ACCTTGTTGGTC---CAAAATGCGAACCCAGATTGTAAGACTATTTTAAA AGCATTGGGACCAGCAGCTACACTAGAAGAAATGATGACAGCATGTCAGG GAGTGGGAGGTCCCGGCCATAAGGCAAGAGTTTTGGCGGAAGCAATG--- ---------AGCCAAGTGACAAAT---------------------TCAGC TACCATAATGATGCAGAAA---GGCAAT---TTTAGGAAC---CAAAGA- --AAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACATAGCCCGA AATTGCAGGGCCCCTAGGAAGAAGGGCTGTTGGAGATGTGGAAAGGAAGG ACACCAAATGAAAGATTGTACT---------GAA---AGACAGGCTAATT TTTTAGGGAAAATCTGG---CCT---TCCCACAAG---------GGA--- AGGCCAGGGAATTTTCTTCAGAGC-------------------------- ----AGACCA------GAGCCGACAGCC---------------------- -----------------------------CCACCAGCA---GAGAGCTTC AGGTTTGGG---------------GAAGAGACAACAACTCCCTCT----- -------------------CAGAAGCAGGAGACA---------------- --------ATAGACAAG---------------------GAACTATAT--- ------CCT---TTA---ACTGCCCTCAAATCACTCTTTGGCAACGACCC CTCGTCACAATAA >Ref.B.US.98.1058_11.AY331295 ------------GCGTCAGTATTAAGCGGGGGAAAATTAGATACATGGGA GAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATA TAGTATGGGCAAGCAGGGAGCTAGAACGATTTGCACTTAACCCTGGCCTG TTAGAAACAGCAGAAGGCTGTAGACAATTATTGGGACAGCTACAGCCATC CCTTCAAACAGGATCAGAAGAACTTAAATCATTATTTAATACAATAGCAA CCCTCTATTGTGTACATCAAAGGATAGAGGTAAGAGACACCAAAGAGGCT TTAGACAAGATAGAGGAAGAGCAA------------AAC----------- ----------AAA---------------AGTAAG------AAAAAA---- -----------------------------GCACAGCAAGCAGCAGCT--- ------------------------GCAGCTGACACAGGA----------- -------------------------------------------------- -----------------------------AACAGCAGCCAG--------- ---------GTCAGCCAAAATTACCCTATAGTGCAGAACCTCCAAGGGCA AATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAG TAATAGAA---GAGAAGGCTTTTAGCCCAGAAGTAATACCCATGTTTGCA GCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACAC AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAAACCATCAATG AGGAAGCTGCAGAATGGGATAGAATACATCCAGCGCAAGCAGGGCCTATA GCACCAGGCCAGATAAGAGACCCAAGGGGAAGTGACATAGCAGGAACTAC TAGTACCCTTCAGGAACAAATAACATGGATGACA---------AATAATC CACCTATC---CCAGTAGGAGAAATCTATAAAAAATGGATAATCATGGGA TTAAATAAAATAGTAAGGATGTATAGTCCTACCAGCATTCTGGACATAAG ACAAGGACCAAAGGAACCCTTTAGGGACTATGTAGACCGGTTCTATAAAA CTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAA ACCTTGTTGGTC---CAAAACGCGAACCCAGATTGTAAGACTATATTAAA AGCATTAGGACCAGCAGCTACACTAGAGGAAATGATGACAGCATGTCAGG GAGTGGGAGGACCTGGCCATAAAGCAAGAGTTTTGGCTGAAGCAATG--- ---------AGCCAAGTAACAAAT---------------------TCAGG TGCCATAATGATGCAGAAA---GGCAAT---TTTAGGAAC---CAG---- -----GTTGTTAGGTGTTTCAATTGTGGCAAAGTAGGGCACATAGCCAAA AATTGCAGGGCCCCTAGGAAGAAGGGCTGTTGGAAATGTGGAAAAGAAGG ACACCAAATGAAAGATTGTGAT---------CAG---AGACAGGCTAATT TTTTAGGGAAGATCTGG---CCT---TCCCACAAA---------GGA--- AGGCCAGGGAATTTTCTTCAGAGC-------------------------- ----AGACCA------GAGCCAACAGCC---------------------- -----------------------------CCACCAGCA---GAGAGCTTC AGGTTTGGG---------------GAGGAGACAACAACTCCCTCT----- -------------------CAGAAGCAGGAGCCA---------------- --------CAAGAA------------------------TAT--------- ------CCT---TTA---GCTTCCCTCAGATCACTCTTTGGCAACGACCC CTCGTCACAATAA >Ref.C.BR.92.BR025_d.U52953 ATGGGTGCGAGAGCGTCAATATTAAGAGGCGGAAAATTAGATGCTTGGGA AAGAATTAAGTTAAAGCCAGGGGGAAAGAAACACTATATGATGAAACACC TAGTCTGGGCAAGCAGGGAGCTGGAAAGATTTGCACTTGACCCTGGCCTT TTAGAGACATCCGAAGGCTGTAAACAAATAATGAAACAGCTACAACCAGC TCTTCAGACAGGAACAAAGGAACTTATATCATTACATAATACGGTTGCAA CTCTCTATTGTGTACATGAAAAGATAGATGTACGAGACACCAAGGAAGCC TTAGACAAAATAAAGGAAGAACAA------------AAC----------- ----------AAA---------------AGTCAG------CAAAAA---- -----------------------------ACACAGCAGGCAGAAGCG--- ---------------------------GCTGACAAAGGA----------- -------------------------------------------------- --------------------------------------AAG--------- ---------GTCAGTCAAAATTATCCTATAGTACAGAATCTCCAAGGGCA AATGGTACACCAGCCCATATCAGCTAGAACTTTGAATGCGTGGGTAAAGG TAGTAGAG---GAGAAGGCTTTCAGCCCAGAGGTAATACCCATGTTTACA GCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGTTAAATAC AGTGGGGGGACACCAAGCAGCCATGCAAATGTTAAAAGATACCATCAATG AGGAGGCTGCAGAATGGGATAGATTACATCCAGTGCATGCAGGGCCTGTC GCACCAGGCCAAATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTAC CAGTACCCTTCAGGAACAAATAACATGGATGACA---------AATAACC CACCTGTC---CCAGTAGGAGACATCTATAAAAGATGGATAATTCTGGGG TTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAA ACAAGGGCCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTTTAAAA CTCTAAGAGCAGAGCAAGCTACCCAAGATGTAAAAAATTGGATGACAGAT ACCTTGTTGGTC---CAAAATGCGAACCCAGATTGTAAGACCATTTTAAG AGCATTAGGGCCAGGGGCTTCATTAGAAGAAATGATGACAGCATGTCAGG GAGTGGGAGGACCTGGCCACAAAGCAAGAGTGTTGGCTGAGGCAATG--- ---------AGCAAAGTAAAC------------------------AATAC AAACATAATGATGCAAAGA---AGCAAT---TGTAAAGGC---CCTAAA- --AGAACTATTAAATGCTTCAACTGTGGCAAGGAAGGGCACTTAGCCAGA AATTGCAGGGCTCCTAGGAAAAAAGGCTGTTGGAAATGTGGAAAAGAAGG ACACCAAGTGAAAGACTGTACT---------GAG---AGGCAGGCTAATT TTTTAGGGAAAATTTGG---CCT---TCCCACAGG---------GGG--- AGGCCAGGAAATCTTCTTCAGAAC-------------------------- ----AGAACA------GAGCCAACAGCC---------------------- -----------------------------CCACCAGAA---GAGAGCTTC AGGTTTGGG---------------GAAGAGACAACAACTCCCTCT----- -------------------CGGAAGCAGGAGACG---------------- --------ATAGACAAG---------------------GAACTG------ ------CCC---TTA---ACTTCCCTCAAATCACTCTTTGGCAGCGACCC CTTGTCAACATAA >Ref.C.ET.86.ETH2220.U46016 ATGGGTGCGAGAGCGTCAATATTAAGAGGCGAAAAATTAGATGCCTGGGA AAAAATTAAGTTAAGGCCAGGGGGAAAGAAACACTATATGCTGAAACACC TAGTCTGGGCAAACAGGGAGCTGGAAAAATTTGCACTTAACCCTGACCTT TTAGATACATCAGCAGGCTGTAAACAAATAATTAAACAGCTACAACCAGC TCTTCAGACAGGAACAGAGGAACTTAAATCATTATTTAATACAGTGGCAA CTCTCTATTGTGTACATCAAAAGATAGAGATAAAAGACACCAAGGAAGCC TTAGACAAGATAGAGGAAGAACAA------------AAC----------- ----------GAA---------------AGTCAG------CAAAAA---- -----------------------------ACACAGCAGGCAGGAGCA--- ---------------------------GCTGACAGAGGA----------- -------------------------------------------------- --------------------------------------AAG--------- ---------GACAGTCAAAATTATCCTATAGTGCAGAATATGCAGGGGCA AATGGTACATCAGCCCATATCAGCTAGAACTTTGAATGCATGGGTAAAAG TAGTAGAG---GAAAAGGCTTTCAGCCCAGAGGTAATACCCATGTTTACA GCTTTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAATAC AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGACACCATCAATG AGGAGGCTGCAGAATGGGACAGGTTACATCCAGTGCATGCAGGGCCTGTT GCACCAGGCCAAATGAGAGACCCAAGGGGAAGTGACATAGCAGGAACAAC TAGTACCCTTCAGGAACAAATAGCATGGATGACA---------GGGAACC CACCTGTT---CCAGTGGGAGACATCTATAAAAGATGGATAATCCTGGGG CTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAA ACAAGGACCAAAGGAACCTTTTAGAGACTATGTAGACCGGTTCTTTAAAA CCTTAAGAGCTGAACAAGCTACACAAGATGTAAAAAATTGGATGACAGAC ACCTTGTTGGTC---CAAAATGCGAACCCAGATTGTAAAACCATTTTAAG AGCATTAGGGCCAGGGGCTTCATTAGAAGAAATGATGACAGCATGTCAGG GAGTGGGAGGACCTGCCCACAAAGCAAGAGTGTTGGCTGAGGCAATG--- ---------AGCCAAGTAAAC------------------------AATAC AACCATAATGATGCAGAAA---AGCAAT---TTTAAGGGC---CCTAAA- --AGAGCAATTAAATGTTTCAACTGTGGCAAGGAAGGGCACCTAGCCAGA AATTGCAGGGCCCCTAGGAAAAAAGGCTGTTGGAAATGTGGAAAGGAAGG ACACCAAATGAAAGACTGTACC---------GAG---AGACAGGCTAATT TTTTAGGGAGACTTTGG---CCT---TCCAACAAG---------GGA--- AGGCCAGGGAATTTCCTTCAGAGC-------------------------- ----AGACCA------GAGCCAACAGCC---CCACCAGAGAGTCT----- -----CAGACCAGAGCCAAC---AGCC--CCACCACCA---GAGAGCTTC AGGTTCGAG---------------GAA---GCA---ACACCTTCT----- -------------------CCGAAGCAGGAGCTG---------------- --------AAAGACAGG---------------------GAA--------- ------GCC---TTA---ACTTCCCTCAAATCACTCTTTGGCAACGACCA CTTGTTACAATAA >Ref.C.IN.95.95IN21068.AF067155 ATGGGTGCGAGAGCGTCAATATTAAGAGGGGGAAAATTAGATAAATGGGA AAAAATTAGGTTAAGGCCAGGGGGAAAGAAACGCTATATGCTAAAACACC TAGTATGGGCAAGCAGGGAGCTGGACAGATTTGCAGTTAACCCTGGCCTT TTAGAGACAGCAGAAGGCTGTAAACAAATAATAAAACAGCTACAACCAGC TCTTCAGACAGGAACAGAGGAACTTAGATCATTATTCAACACAGTAGCAA CTCTCTATTGTGTACATGCAGGGATAGAAGTACGAGACACCAAAGAAGCC TTAGACAAGATAGAAGAAGAACAA------------AAC----------- ----------AAA---------------ATTAAG------CAAAAA---- -----------------------------ACACAGCAGGCAAAAGAG--- ---------------------------GATGAC---GGG----------- -------------------------------------------------- --------------------------------------AAG--------- ---------GTCAGTCAAAATTATCCTATAGTGCAGAATCTCCAAGGGCA AATGGTACACCAAGCCATATCACCTAGAACTTTGAATGCATGGGTAAAAG TAATAGAG---GAAAAGGCTTTTAGCCCAGAGGTAATACCCATGTTTACA GCATTATCAGAAGGAGCCACCCCACAAGATTTAAATACCATGTTAAATAC AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACCATCAATG AAGAGGCTGCAGAATGGGATAGATTACATCCAGTACCTGCAGGGCCTATT GCACCAGGCCAACTGAGAGAACCAAGGGGAAGTGATATAGCAGGAACTAC TAGTACCCTTCAGGAACAAATAGCATGGATGACG---------AATAACC CACCTGTT---CCAGTGGGAGACATCTATAAAAGATGGATAATTCTGGGG TTAAATAAAATAGTAAGAATGTATAGCCCTGTGAGCATTTTGGACATAAG ACAAGGGCCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTTTAAAA CTTTAAGAGCTGAACAAGCTACACAAGATGTAAAAAATTGGATGACAGAA ACCTTGTTGGTC---CAAAATGCGAATCCAGATTGTAAGACCATTTTAAG AGCATTAGGACCAGGGGCTTCATTAGAAGAGATGATGACAGCATGTCAGG GAGTGGGAGGACCTAGCCACAAAGCAAGAGTGTTGGCTGAGGCAATG--- ---------AGCCAAACAAAC---------------------------AG TGCCATACTGATGCAAAGA---AGCAAT---TTTAAAGGC---TCTAAA- --AGAATTGTTAAATGTTTCAACTGTGGCAAGGAAGGGCACCTAGCCAGA AATTGCAGGGCCCCTAGGAAAAAAGGCTGTTGGAAATGTGGAAAGGAAGG ACACCAAATGAAAGACTGTACT---------GAA---AGGCAGGCTAATT TTTTAGGGAAAATTTGG---CCT---TCCCACAAG---------GGG--- AGGCCAGGGAATTTCCTCCAGAGT-------------------------- ----AGACCA------GAGCCAACAGCT---------------------- -----------------------------CCACCAGCA---GAGAGCTTC AGGTTCGAG---------------GAG---ACA---ACCCCAGCT----- -------------------CCGAAGCAGGAGCCG---------------- --------AAAGACAGG---------------------GAA--------- ------CCT---TTA---ACTTCCCTCAGATCACTCTTTGGCAGCGACCC CTTGTCTCAATAA >Ref.C.ZA.04.04ZASK146.AY772699 ATGGGTGCGAGAGCGTCAGTATTAAGAGGCGAAAAATTAGATACATGGGA AAAAATTAGGTTAAGGCCAGGGGGAAAGAAACACTATATGCTAAAACACA TAGTATGGGCAAGCAGGGAGCTGGAAAGATTTGCACTCAACCCTGGCCTT TTAGAAACATCAGAAGGCTGTAAACAAATATTGGCACAAATACAACCAGC TATTCAGACAGGAACAGAGGAACTTAAATCATTATTCAACACAATAGCAG TTCTCTATTGTGTACATAAAAAGATAGATGTAAGAGACACCAAGGAAGCC TTAGACAAGATAGAGGAAGAGCAA------------AAC----------- ----------AAA---------------AGTCAG------CAAAAA---- -----------------------------ACACAGCAGGCAAAAGCG--- ---------------------------GCTGAC---GAA----------- -------------------------------------------------- --------------------------------------AAG--------- ---------GTCAGTCAAAATTTTCCTATAGTACAGAATCTTCAAGGGCA AATGGTACATCAACCCCTATCACCTAGAACCTTGAATGCATGGGTAAAAG TAATAGAG---GAGAAGGGTTTTAACCCAGAGGTAATACCCATGTTTACA GCATTATCAGAGGGAGCCACCCCACAAGATTTGAACACCATGCTAAATAC GGTGGGGGGACATCAAGCAGCCATGCAGATGTTAAAAGATACCATCAATG AAGAGGCTGCAGAATGGGATAGATTACATCCAGTACATGCAGGGCCTGTC GCACCAGGCCAAATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTAC TAGTAACCTTCAGGAACAAGTAGCATGGATGACA---------AGTAACC CACCTATT---CCAGTGGGAGACATCTATAAAAGATGGATAATTCTGGGA TTAAATAAAATAGTGAGGATGTATAGCCCGGTCAGCATTTTGGACATAAA ACAAGGGCCAAAGGAACCCTTTAGAGACTATGTAGATCGGTTCTTTAAAA CTTTAAGAGCTGAACAAGCTACACAAGAGGTAAAAAATTGGATGACAGAC ACCTTGTTGGTC---CAAAATGCGAACCCAGATTGTAAGACCATTTTAAG AGCATTAGGACCAGGGGCTACATTAGAAGAAATGATGGCAGCATGTCAAG GGGTGGGAGGACCTGGCCACAAGGCAAGAGTGTTGGCTGAGGCAATG--- ---------AGCCAAATAAAC------------------------AATGG AAACATAATGATGCAGAGA---AGTAAT---TTTAAAGGC---CCTAAA- --AGAATTGTTAAATGTTTTAACTGTGGCAAGGGGAGGCACATAGCCAAA AATTGCAGGGCCCCTAGGAAAAAAGGCTGTTGGAAATGTGGAAAGGAAGG ACACCAAATGAAAGACTGTACT---------GAA---AGGCAGGCTAATT TTTTAGGGAAAATTTGG---CCT---TCCCAGAAG---------GGG--- AGGCCAGGGAATTTTCTCCAGAAC-------------------------- ----AGACTA------GAGCCAACAGCC---------------------- -----------------------------CCACCAGCA---GAGAGCTTC AGGTTCGAG---------------GAG---ACG---ACCCCTGCT----- -------------------CCGAAACAGGAGCTG---------------- --------AAAGACAGG---------------------GAA--------- ------CCT---TTA---ACTTCCCTCAGATCACTCTTTGGCAGCGACCC CTTGTCTCAATAA >Ref.D.CD.83.ELI.K03454 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATAAATGGGA AAAAATTCGGTTACGGCCAGGAGGAAAGAAAAAATATAGACTAAAACATA TAGTATGGGCAAGCAGGGAGCTAGAACGATATGCACTTAATCCTGGCCTT TTAGAAACATCAGAAGGCTGTAAACAAATAATAGGGCAGCTACAACCAGC TATTCAGACAGGAACAGAAGAACTTAGATCATTATATAATACAGTAGCAA CCCTCTATTGTGTACATAAAGGAATAGATGTAAAAGACACCAAGGAAGCT TTAGAAAAGATGGAGGAAGAGCAA------------AAC----------- ----------AAA---------------AGTAAG------AAAAAG---- -----------------------------GCACAGCAAGCAGCAGCT--- ------------------------------GACACAGGA----------- -------------------------------------------------- -----------------------------AACAACAGCCAG--------- ---------GTCAGCCAAAATTATCCTATAGTGCAGAACCTACAGGGGCA AATGGTACATCAGGCCATATCACCTAGAACTTTGAACGCATGGGTAAAAG TAATAGAA---GAAAAGGCTTTCAGCCCAGAAGTAATACCCATGTTTTCA GCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACAC AGTGGGGGGACATCAAGCAGCCATGCAAATGCTAAAAGAGACCATCAATG AAGAAGCTGCAGAATGGGATAGGTTACATCCAGTGCATGCAGGGCCTATT GCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGATATAGCAGGAACTAC TAGTACCCTTCAGGAACAAATAGCATGGATGACA---------AGTAACC CACCTATC---CCAGTAGGAGAAATCTATAAAAGATGGATAATTGTGGGA TTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAG ACAGGGACCAAAGGAACCTTTTAGAGACTATGTAGACCGGTTCTATAAAA CTCTAAGAGCCGAGCAAGCTTCACAGGATGTAAAAAATTGGATGACAGAA ACCTTGTTGGTC---CAAAATGCAAACCCAGATTGCAAGACTATCTTAAA AGCATTGGGACCACAGGCTACACTAGAAGAAATGATGACAGCATGTCAGG GAGTGGGGGGGCCCAGCCATAAAGCAAGAGTTCTGGCTGAGGCAATG--- ---------AGCCAAGCAACAAATTCA------------------GTTAC TACAGCAATGATGCAGAGA---GGCAAT---TTTAAGGGC---CCAAGA- --AAAATTATTAAGTGTTTCAATTGTGGCAAAGAAGGGCACATAGCAAAA AATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAGATGTGGAAAGGAAGG ACACCAACTAAAAGATTGCACT---------GAG---AGACAGGCTAATT TTTTAGGGAGAATTTGG---CCT---TCCCACAAG---------GGA--- AGGCCGGGGAACTTTCTCCAAAGC-------------------------- ----AGACCA------GAGCCAACAGCC---------------------- -----------------------------CCACCAGCA---GAGAGCTTC GGGTTTGGG---------------GAAGAGATA---ACCCCCTCT----- -------------------CAAAAACAGGAGCAG---------------- --------AAAGACAAG---------------------GAACTGTAT--- ------CCT---TTA---ACTTCCCTCAAATCACTCTTTGGCAACGACCC CTTGTCGCAATAA >Ref.D.CM.01.01CM_4412HAL.AY371157 ------GCGAGAGCGTCAATATTAAGCGGGGGAAAATTGGATGCATGGGA AAAAATTCGGTTACGGCCAGGGGGAAGCAAAAAGTATAGGCTAAAACATC TAATATGGGCAAGCAATGAGCTAGAACGATTTGCACTTAATCCTGGCCTT TTAGAGACATCAGATGGCTGTAAACAAATACTAGGCCAGCTACAACCAGC TCTTAAAACAGGAACAGAAGAACTTAGATCATTATTTAATGCAGTAGCAG TACTCTATTGTGTACATGAAAGGATAGAGGTAAAGGACACCAAGGAAGCC TTAGACAAGATAGAGGAAGAACAA------------AAC----------- ----------AAA---------------AGTAAG------AAAAAA---- -----------------------------GCACAGCAAGCAGCAGCT--- ------------------------------GACACAGGG----------- -------------------------------------------------- -----------------------------GACAACAAACAG--------- ---------GTCAGCCAAAATTATCCTATAGTGCAGAACTTACAGGGGCA AATGGTACACCAAGCCCTATCACCCAGAACCTTGAACGCATGGGTAAAAG TAATAGAG---GAAAAGGCTTTCAACCCAGAAGTAATACCCATGTTTTCA GCATTATCAGAAGGAGCCACCCCACAGGATTTAAATACCATGCTAAACAC AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATG AGGAAGCTGCAGAATGGGACAGGCTACATCCAGTGCAAGCAGGGCCTGTT GCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGATATTGCAGGAACTAC TAGTACCCTTCAGGAACAAATAGGGTGGATGACA---------AGTAATC CACCAATC---CCAGTAGGGGAAATCTATAAAAGATGGATAATCTTGGGA TTGAATAAAATAGTAAGAATGTATAGCCCTGTCAGTATTTTGGATATAAG ACAAGGACCAAAAGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAA CTCTAAGAGCCGAGCAAGCTACACAGGAAGTAAAAAATTGGATGACAGAA ACCTTGTTGGTT---CAAAATGCAAACCCAGACTGTAAAACTATCTTAAA GGCGTTGGGGCCAGGGGCTACACTAGAAGAAATGATGACAGCATGTCAGG GAGTGGGAGGGCCCGGCCATAAAGCAAGAGTTTTGGCTGAGGCAATG--- ---------AGCCAAGCAACAGCAGGT------------ATG---AATGC TGCAATAATGATGCAGAGG---GGCAAT---TTTAAGGGC---CCAAAG- --AGAATTGTTAAGTGTTTCAACTGTGGCAAAGAAGGGCACATAGCAAAA AATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAGAGAAGG ACACCAAATGAAAGATTGCACA---------GAA---AGACAGGCTAATT TTTTAGGGAAAATTTGG---CCT---TCCAACAAG---------GGA--- AGGCCAGGGAACTTTCTTCAGAGC-------------------------- ----AGACCA------GAGCCAACAGCC---------------------- -----------------------------CCACCAGCA---GAGAGCTTC GGGTTCGGG---------------GAGGAGATA---GCCCCCTCT----- -------------------CAGAAACAGGAGCAG---------------- --------AAAGACAAAGACCAG---------------GAACTGTAT--- ------CCT---TTA---ACTTCCCTCAAATCACTCTTTGGCAACGACCC CTTGTCACAATAA >Ref.D.TZ.01.A280.AY253311 ------GCGAGAGCGTCAGTATTAAGCGGGGGACAATTAGATGCATGGGA AAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATCAACTAAAACATA TAGTATGGGCAAGCAGGGAGTTAGAACGATTTGCACTTAATCCTGGCCTT TTAGAGACATCCGAAGGCTGTAAACAAAT----------CTACAACCAGC TATTCAGACAGGATCAGAAGAACTTAAATCATTATTTAATACAGTAGCAA CCCTCTATTGTGTGCATAGAAAGATAGAGGTAAAAGACACCAAGGAAGCT TTAGAAAAATTAGAGGAAGAGCAA------------ACC----------- ----------AAA---------------AGTAAG------AAAAAG---- -----------------------------GCACAGCAAGCAACAGCT--- ------------------------------GACACAGGA----------- -------------------------------------------------- -----------------------------AGCAGCAGCCAG--------- ---------GTCAGCCAAAATTATCCTATAGTGCAAAACCTACAGGGGCA AATGGTACACCAGGCCATATCACCTAGAACCTTGAACGCATGGGTAAAAG TAATAGAA---GAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCA GCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACAATGCTAAACAC AGTGGGGGGACATCAAGCAGCTATGCAAATGTTAAAAGAGACCATCAATG AGGAAGCTGCAGAATGGGATAGGCTACATCCAGTGCATGCAGGGCCTATT GCACCAGGACAGATGAGAGAACCAAGGGGAAGTGATATAGCAGGAACTAC TAGTACCCTTCAGGAACAAATAGCATGGATGACA---------AATAATC CACCTGTC---CCAGTAGGAGAAATATATAAAAGATGGATAATCCTGGGA TTAAATAAAATAGTAAGAATGTATAGCCCTGTTAGCATTTTGGACATAAG ACAAGGACCAAAGGAGCCCTTTAGGGACTATGTAGATCGGTTCTATAAAA CTCTAAGAGCCGAGCAAGCTTCACAAGATGTAAAAAATTGGATGACTGAA ACCTTGTTGGTC---CAAAATGCGAACCCAGATTGTAAAACTATCTTAAA AGCATTGGGACCAGCGGCTACATTAGAAGAAATGATGACAGCATGTCAGG GAGTGGGGGGACCCAGTCATAAGGCAAGAGTTCTAGCTGAGGCAATG--- ---------AGCCAAGCAACAAATGTA------------------AATGC TGCCATAATGATGCAGAGA---GGTAAT---TTTAAGGGC---CCAAGG- --AAAATCATTAAGTGTTTCAACTGTGGCAAAGAAGGACACATAGCAAAA AATTGCAGGGCCCCAAGAAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGG ACACCAAATGAAAGATTGCACT---------GAA---AGACAGGCTAATT TTTTAGGGAAAATTTGG---CCT---TCCCACAAA---------GGA--- AGGCCAGGGAACTTCCTTCAGAGC-------------------------- ----AGACCA------GAGCCAACAGCC---------------------- -----------------------------CCACCAGCA---GAGATCTTC GGGTTTGGG---------------GAGGAGATA---AAACCCTCT----- -------------------CAGAAACAGGAGCAG---------------- --------AAAGACAAG------------GACAAG---GAACTGTAT--- ------CCT---TCA---GCTTCCCTCAAATCACTCTTTGGCAACGACCC CTTGTCACAATAA >Ref.D.UG.94.94UG114.U88824 ATGGGTGCGAGAGCGTCAGTATTAAGCGGAGGAAAATTAGATGAATGGGA AAAAATTCGGTTACGGCCAGGGGGAAAGAAAAAATATAGACTAAAACATC TAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCACTTAATCCTGGCCTT TTAGAAACATCAGAAGGCTGTAGACAAATAATAAGACAGCTACAACCATC TATTCAGACAGGATCAGAGGAAATTAAATCATTATATAATACAGTGGTAA CCCTCTATTGTGTACATGAGAGGATAAAGGTAGCAAGCACCAAGGAAGCT TTAGACAAGATAGAGGAAGAACAA------------GCC----------- ----------AAA---------------AGTAAG------AAAAAA---- -----------------------------GCACAGCAAGCAACAGCT--- ------------------------------GACACAAGA----------- -------------------------------------------------- -----------------------------AACAGCAGCCAG--------- ---------GTCAGCCAAAATTATCCTATAGTGCAAAACCTACAGGGGCA AATGGTACACCATCCCCTATCACCTAGAACTTTGAACGCATGGGTAAAAG TAATAGAG---GAGAAGGCTTTCAACCCAGAAGTAATACCCATGTTTTCA GCATTATCAGAAGGAGCCACCCCACAAGATTTAAATACCATGCTAAACAC AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAGGATACCATCAATG AGGAAGCTGCAGAATGGGATAGGCTACATCCAGTGCATGCAGGGCCTGTT GCACCAGGCCAATTGAGAGAACCAAGGGGAAGTGATATAGCAGGAACTAC TAGTAACCTTCAGGAACAAATAGGATGGATGACA---------AGCAATC CACCTATC---CCAGTAGGAGAAATCTATAAAAGATGGATAATCCTAGGA TTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAG ACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGATCGGTTCTATAAAA CTCTAAGAGCCGAGCAAGCTTCACAGGATGTAAAAAATTGGATGACTGAA ACCTTGTTGGTC---CAAAATGCGAACCCAGATTGTAAAACTATCTTAAA AGCATTGGGACCAGCGGCTACATTAGAAGAAATGATGACAGCATGTCAGG GAGTGGGGGGACCCAGTCATAAAGCAAGAGTTTTGGCTGAGGCAATG--- ---------AGCCAAGCAACAAATGCA------------------AATAC TGCTATAATGATGCAGAGA---GGCAAT---TTTAAGGGC---CCAAAG- --AAAATCATTAAGTGTTTCAACTGTGGCAAAGAAGGGCACACGGCAAAA AATTGCAGGGCTCCTAGAAAAAAGGGCTGTTGGAAATGTGGAAGGGAAGG ACACCAAATGAAAGATTGCACT---------GAA---AGACAGGCTAATT TTTTAGGGAAAATTTGG---CCT---TCCCACAAT---------GGA--- AGGCCAGGGAATTTCCTTCAGAGC-------------------------- ----AGACCCCCAGCAGAGCCAACAGCC---------------------- -----------------------------CCACCAGCA---GAGATCTTC GGATTAGGG---------------GAGGAGATA---ACACCTCCT----- -------------------CAGAAACAGGAGCAG---------------- --------AAAGACAAG---------------------GAACTGTAT--- ------CCT---TTA---ACCTCCCTCAAATCACTCTTTGGCAACGACCC GTTGTCACAGTAA >Ref.F1.BE.93.VI850.AF077336 ATGGGTGCGAGAGCGTCAATATTAAGCGGGGGAAAATTAGATGAATGGGA AAAAATTCAGTTAAGGCCGGGGGGAAAGAAAAGATATAAAATGAAACATC TAATATGGGCAAGCAGGGAGCTAGAACGATTTGCACTTGATCCTGGCCTT CTAGAAACATCAGAAGGCTGTCAAAAAATAATAAGACAGCTACAACCATC CCTTCAGACAGGATCAGAAGAGCTTAAGTCATTATTTAATACAGTAGCAG TCCTCTATTATGTACATCAAAGGGCAGGGGTAACAGACACCAAGGAAGCT TTAGACAAGCTAGAGGAAGAACAA------------AAC----------- ----------AAA---------------AGTCAG------CAAAAG---- -----------------------------ACACAGCAAGCGGCAGCT--- ------------------------------GACAAAGGG----------- -------------------------------------------------- -------------------------------------------------- ---------GTCAGTCAAAATTACCCTATAGTACAGAATCTTCAGGGACA AATGGTACACCAGTCTCTATCACCTAGAACTTTAAATGCATGGGTAAAGG TGATAGAA---GAGAAGGCTTTTAGCCCAGAAGTAATACCCATGTTTTCA GCATTATCAGAAGGGGCCACTCCCACAGATTTAAACACCATGCTAAATAC AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGACACCATCAATG AGGAAGCTGCAGAATGGGACAGATTACATCCAGTGCATGCAGGGCCTGCC CCACCAGGCCAGATGAGGGAACCTAGGGGGAGTGATATAGCTGGAACTAC TAGTACCCTTCAGGAACAAATACAATGGATGACG---------GGCAACC CACCTGTC---CCAGTGGGAGACATCTATAAAAGATGGATCATCCTAGGA TTAAATAAAATAGTAAGAATGTATAGTCCTGTCAGCATTTTGGACATAAA ACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGATTCTTTAAAG TCCTAAGAGCTGAGCAAGCTTCACAGGACGTAAAGGGTTGGATGACAGAC ACATTGTTGGTC---CAAAATGCGAACCCAGATTGTAAGACCATTTTAAA AGCATTGGGAACAGGGGCTACACTAGAAGAAATGATGACAGCATGTCAGG GAGTGGGAGGACCTAGCCATAAGGCAAGAGTTTTGGCCGAGGCAATG--- ---------AGTCAAGCAAAT---------------------------TC AGCCATAATGATGCAGAAA---AGTAAT---TTTAAGGGC---CAAAGA- --AGAGTTGTTAAATGTTTTAATTGTGGCAAAGAAGGACACATAGCCAGA AATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAATGTGGAAGAGAAGG ACACCAAATGAAAGACTGCACT---------GAA---AGACAGGCTAATT TTTTAGGGAAAATTTGG---CCT---TCCAACAAG---------GGG--- AGGCCCGGAAATTTCCTTCAGAGC-------------------------- ----AGACCA------GAGCCAACAGCC---------------------- -----------------------------CCACCAGCA---GAGAGCTTC GGGTTCAGA---------------GAGGAGATA---ACCCCCTCT----- -------------------CCGAAGCAGGAGCAG---------------- --------AAAGACGGG---------------------GAACTGTAC--- ---CCTCCC---TTA---GCTTCCCTCAAATCACTCTTTGGCAACGACCC TTAGTCACAATAA >Ref.F1.BR.93.93BR020_1.AF005494 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCTTGGGA AAAAATTCGGTTAAGGCCGGGGGGAAAGAAAAAATATAGACTAAAACATC TAGTATGGGCAAGCAGGGAGCTAGAACGATTTGCACTTGATCCAGGCCTT CTAGAAACATCAGAAGGCTGTCGAAAAATAATAGGACAGTTACAACCATC CCTTCAGACAGGATCAGAAGAGCTCAAATCATTATATAATACAATAGCAG TCCTCTATTATGTACATCAAAAGGTAGAGGTAAAAGACACCAAGGAGGCT TTAGAGAAGCTAGAGGAAGAACAA------------AAC----------- ----------AAA---------------GGTCGG------CAAAAG---- -----------------------------ACACAGCAAGCGACTGCT--- ------------------------------GAAAAAGGG----------- -------------------------------------------------- -------------------------------------------------- ---------GTCAGTCAAAATTACCCTATAGTACAGAATCTTCAGGGACA AATGGTACACCAGTCTTTATCACCTAGAACTTTAAATGCATGGGTAAAGG TGATAGAA---GAGAAGGCTTTTAGTCCAGAAGTAATACCCATGTTTTCA GCATTATCAGAAGGGGCCACTCCACAAGATTTAAACACCATGTTAAATAC AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGACACCATCAATG AGGAGGCTGCAGAATGGGACAGATTACATCCAACACAGGCAGGACCCATC CCCCCAGGTCAGATAAGGGAACCTAGGGGAAGTGATATAGCTGGAACTAC TAGTACCCTTCAGGAACAAATACAATGGATGACA---------GGCAACC CACCTGTC---CCAGTGGGAGAAATGTATAAAAGATGGATCATCCTAGGA TTAAATAAAATAGTAAGAATGTATAGCCCTGTCGGCATTTTGGACATAAG ACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTCTTTAAAA CCCTAAGAGCTGAGCAAGCTACACAGGAAGTAAAGGGTTGGATGACAGAC ACCTTGTTGGTC---CAAAATGCGAACCCAGATTGTAAGACCATTTTAAA AGCATTGGGACCAGGGGCTACACTAGAGGAAATGATGACAGCATGTCAGG GAGTGGGAGGACCTAGCCATAAGGCAAGAGTTTTGGCTGAGGCAATG--- ---------AGCCAAGCAACA------------------------AATAC AGCTATAATGATGCAGAAA---AGTAAC---TTTAAGGGC---CAAAGA- --AGAATTGTTAAATGCTTTAATTGTGGCAAAGAAGGACACATAGCCAAA AATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAGTGTGGAAGAGAGGG ACACCAAATGAAGGACTGCACT---------GAG---AGACAGGCTAATT TTTTAGGGAAAATTTGG---CCT---TCCAACAAG---------GGG--- AGGCCCGGAAACTTCATCCAGAAC-------------------------- ----AGGCCA------GAGCCGTCAGCC---------------------- -----------------------------CCGCCAGCA---GAGAGCTTC AGGTTCGGG---------------GAGGAGACA---ACCCCATCT----- -------------------CCGAAGCAGGAGCAG---------------- --------AAAGACGAG---------------------GGACTGTAC--- ---CCTCCC---TTA---GCTTCCCTCAAATCACTCTTTGGCAACGACCC CTAGTCACAATAA >Ref.F1.FI.93.FIN9363.AF075703 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAACTAGATGCATGGGA AAAAATTCGGTTAAGGCCGGGGGGAAAGAAACAATATAGAATAAAACATC TAGTATGGGCAAGCAGGGAGCTAGAACGATTTGCAATAGATCCTGGCCTT CTAGAAACATCAGAAGGCTGTCAAAAAATAATAGCACAGATACAGCCATC CATTCAGACAGGATCAGAAGAGCTTAGATCATTATATAACACAATAGCAG TCCTCTATTTTGTACATCAAAAGATAGAGGTAAAGGACACCAAGGAAGCT TTAGATAAGCTAGAGGAAGAACAA------------AAC----------- ----------AAA---------------AGTCAG------CAAAAG---- -----------------------------ACACAGCAAGCGGCAGCT--- ------------------------GCAGCTGACAAAGGG----------- -------------------------------------------------- -------------------------------------------------- ---------GTCAGTCAAAATTACCCTATAGTACAGAATCTTCAGGGACA AATGGTACATCAGGCTATATCACCTAGAACTTTAAATGCATGGGTAAAGG TGATAGAA---GAGAAGGCTTTTAGCCCAGAAGTTATACCCATGTTTTCA GCATTATCAGAAGGGGCCACTCCACAAGATTTAAACACCATGCTAAATAC AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGACACCATTAATG AGGAAGCTGCAGAATGGGACAGATTACATCCAGTGCATGCAGGACCTATT CCACCAGGCCAGATGAGGGAACCTAGGGGAAGCGATATAGCTGGAACTAC TAGTACCCTTCAGGAACAAATACAATGGATGACA---------AGTAACC CACCTGTC---CCAGTGGGAGACATCTATAAAAGATGGATCATCCTAGGA TTAAATAAAATAGTAAGGATGTATAGCCCTGTCAGCATTTTGGACATAAG ACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTCTTTAAAG CTCTAAGAGCTGAGCAAGCTACACAGGAAGTAAAGGGTTGGATGACAGAC ACCTTGTTGGTC---CAAAATGCGAATCCAGATTGTAAGATCATTTTAAA AGGATTGGGAATAGGGGCTACACTAGAAGAAATGATGACAGCATGTCGGG GAGTGGGAGGACCTGGCCATAAGGCAAGAATTTTGGCTGAGGCAATG--- ---------AGCCAAGCAAAT---------------------------AC AACCATAATGATGCAGAAA---AGTAAT---TTTAGGGGC---CAAAGA- --AGAATTGTTAAATGTTTTAATTGTGGCAAAGAAGGACACATAGCCAGA AATTGCAGGGCCCCCAGGAAAAAGGGCTGTTGGAAATGTGGACAAGAAGG GCACCAAATGAAAGACTGCACT---------GAA---AGACAGGCTAATT TTTTAGGGAAAATTTGG---CCT---TCCAACAAG---------GGG--- AGGCCCGGAAATTTCCTTCAGAGT-------------------------- ----AGACCA------GAGCCAACAGCC---------------------- -----------------------------CCGCCAGCA---GAGAGCCTC GGGATCAGA---------------GAAGAGGTA---ACTCCCTCT----- -------------------CCGAGGCAGGAGCAG---------------- --------AAAGAAGAG---------------------GGACAGTAC--- ---CCTCCC---TTA---GCTTCCCTCAAATCACTCTTTGGCAACGACCC CTAGTCACAATAA >Ref.F1.FR.96.96FR_MP411.AJ249238 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCATGGGA AAGAATTCGATTAAGACCGGGGGGAAAGAAAAAATATAGAATGAAGCATC TAGTATGGGCAAGCAGGGAGTTAGAACGATTTGCAGTTGATCCTGGACTT CTAGAAACACCAGAAGGCTGTAAGCAAATAATAAGACAGCTACAACCATC CCTTCAGACAGGATCAGAAGAGCTTAGATCATTGTTCAATACAGTAGCAG TTCTCTATTGTGTACATCAAAAGATAGAGATAAAGGACACCAAGGAAGCT TTAGAGAAGTTAGAGGAGGAACAA------------AAC----------- ----------AAA---------------GGTCAG------CAAAAG---- -----------------------------ACACAGCAAGCGGCAGCT--- ------------------------------GACAAAGGA----------- -------------------------------------------------- -------------------------------------------------- ---------GTCAGTCAAAATTACCCTATAGTACAAAATCTTCAGGGACA GATGGTACATCAGCCTATATCACCTAGAACTTTAAATGCATGGGTAAAAG TGATAGAA---GAGAAGGCTTTTAGCCCAGAAGTAATACCCATGTTCTCA GCATTATCAGAAGGGGCCACCCCACAAGATTTAAACACCATGCTAAATAC AGTGGGTGGACATCAAGCAGCCATGCAAATGTTAAAAGACACCATCAATG AGGAAGCTGCAGAATGGGACAGATTACATCCAGCGCATGCAGGGCCTATC CTACCAGGCCAGATGAGAGAACCTAGGGGTAGTGACATAGCTGGAACTAC TAGTACCCTTCAGGAACAAATACAATGGATGACA---------AGCAACC CACCTGTC---CCAGTGGGAGACATCTATAAAAGATGGATCATCCTAGGA TTAAATAAAATAGTAAGAATGTATAGCCCTGTTAGCATTTTGGACATAAG ACAAGGGCCAAAGGAACCTTTTAGAGACTATGTGGACAGGTTCTTTAAAA CTCTAAGAGCTGAGCAAGCTTCACAGGAAGTAAAGAATTGGATGACAGAA AGCTTGCTGGTG---CAAAATTCGAACCCAGACTGTAAGACCATCTTAAA AGCATTAGGACCAGGGGCTACACTAGAAGAAATGATGACAGCATGTCAGG GAGTGGGAGGACCTGGCCATAAGGCAAGGGTTTTGGCTGAGGCCATG--- ---------AGCCAAGCAACA------------------------AATGC AGCTATAATGATGCAGAAA---AGTAAC---TATAAGGGC---CCAAGA- --AGATTTATTAAATGTTTTAATTGTGGCAAAGAAGGACACATAGCCAAA AATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAATGTGGAAAAGAAGG ACATCAAATGAAAGACTGCACT---------GAA---AGACAGGCTAATT TTTTAGGGAAAATTTGG---CCT---TCCAACAAG---------GGG--- AGGCCCGGAAATTTTCTTCAGAAC-------------------------- ----AGGCCA------GAGCCAACAGCC---------------------- -----------------------------CCGCCAGCG---GAGAGCTTC GGGTTCAAA---------------GAGGAAATA---ACCCCCTCT----- -------------------CCGAAGCAGGAGCAG---------------- --------AAGGACGAG------------GGACAG---GGACTGTAT--- ---CCTCCC---TTA---GCCTCCCTCAAATCACTTTTTGGCAGCGACCC TTAGTCACCATAA >Ref.F2.CM.02.02CM_0016BBY.AY371158 ------GCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGACTGGGA GAAAATTCGGTTAAGGCCGGGAGGGAAGAAAAAATATAGGCTAAAACATA TAGTATGGGCAAGCAAGGAGCTAGAACGATTTGCACTTAATCCTGGCCTT TTAGAGACAACAGAAGGCTGTAAACAAATAATAGGACAACTACAATCATC CCTTCAGACAGGATCAGAAGAGATTAAATCATTATATAACACAGTAGCAG TCCTCTATTATGTACATCAAAAGATACAAATAAGAGACACCAAGGAAGCT TTAGATAAGCTACAGGAAGAACAA------------GAC----------- ----------AAA---------------TATCAG------CAAAAA---- -----------------------------ACACAACCAGCAGCGGCT--- ------------------------------GATAAAGGG----------- -------------------------------------------------- -------------------------------------------------- ---------GTCAGTCAAAATTACCCTATAGTACAGAATCTTCAGGGGCA AATGGTACATCAGGCTATATCACCTAGAACTCTAAATGCATGGGTAAAAG TAATAGAA---GAGAAGGCTTTCAGCCCAGAAGTCATACCCATGTTTTCA GCATTATCAGAAGGGGCCACCCCACAAGATTTAAACACCATGCTAAACAC AGTAGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACCATCAATG AGGAAGCTGCAGAATGGGACAGGTTACATCCAGTGCAGGCAGGACCTATC CCACCAGGTCAGATAAGAGAACCTAGGGGAAGTGATATAGCAGGAACTAC TAGTACCCTTCAGGAACAAATAGCATGGATGACA---------AGCAACC CACCTGTC---CCAGTAGGAGAAATTTATAAAAGATGGATAATCCTAGGA TTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAG ACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTCTTTAAAA CTCTAAGAGCTGAGCAAGCTACACAGGAAGTAAAAGGCTGGATGACAGAC ACCTTGTTGGTC---CAAAATGCGAACCCAGATTGTAAGACCATTTTAAA AGCACTAGGACCAGGGGCTACACTAGAAGAAATGATGACAGCATGTCAGG GAGTGGGAGGACCTGGCCATAAAGCAAGAATTTTGGCTGAGGCAATG--- ---------AGCCAAGTAACA------------------------GCTAC ATCCGTACTGATGCAGAAA---AGCAAC---TTTAAGGGC---CAAAAA- --AGAATTGTCAAGTGTTTCAACTGTGGCAAAGAAGGACATATAGCTAAA AATTGCAGGGCCCCTAGAAAAAGGGGCTGTTGGAAATGTGGAAAGGAAGG ACACCAAATGAAAGACTGCACT---------GAA---AGACAGGCTAATT TTTTAGGGAAAATTTGG---CCT---TCCAACAAA---------GGG--- AGGCCTGGGAATTTCATTCAGAGC-------------------------- ----AGACCA------GAGCCAACGGCC---------------------- -----------------------------CCGCCAGCA---GAGGGCTTC GGGTTCGGA---------------GAAGAGATA---ACTCCCTCC----- -------------------CCGAAGCAGGAGCAG---------------- --------AAAGACAAG---------------------GGACTGTAT--- ---CCTCCC---TTG---ACTTCCCTCAAATCACTCTTTGGCAACGACCC GTAGTCACAATAA >Ref.F2.CM.95.95CM_MP255.AJ249236 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCATGGGA AAAAATTCGGTTAAAGCCGGGGGGAAAGAAAAGATATAGGCTAAAACATC TAGTATGGGCAAGCAGGGAACTAGAACGATTTGCACTTAATCCTAGCCTT TTAGAAACAACAGAAGGCTGTAAGAAAATAATAGGACAATTACAATCATC CCTTCAGACAGGATCAGAAGAGCTTAAATCACTATACAATGCAGTAGTAG TTCTCTATTATGTACATCAAAGGATAGATGTAAGAGACACCAAGGAAGCT TTAGATAAGCTACAGGAAGAACAA------------GAT----------- ----------AAA---------------AGTCAG------CAAAAG---- -----------------------------GAACAACAAAAGGCGGCT--- ------------------------------GACAAAGAG----------- -------------------------------------------------- -------------------------------------------------- ---------GTCAGTCAAAATTACCCTATAGTGCAGAATATTCAGGGGCA AATGGTACACCAGGCTCTATCACCTAGAACTTTAAATGCATGGGTAAAAG TAATAGAA---GAGAAGGCTTTCAGTCCAGAAGTAATACCCATGTTTTCA GCATTATCAGAAGGGGCCACCCCACAAGATTTAAATACCATGCTAAACAC AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACTATCAATG AGGAGGCTGCAGAATGGGACAGGTTACATCCAGTGCATGCAGGGCCTATC CCACCAGGGCAGATGAGAGAACCTAGGGGAAGTGATATAGCAGGAACTAC TAGTACCCTTCAGGAACAAATAACATGGATGACA---------GGCAACC CACCCGTC---CCAGTAGGAGAAATCTATAAAAGATGGATAATCCTAGGA TTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAA ACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTCTTTAAAA CTCTAAGAGCTGAACAAGCTACACAGGAGGTAAAAAACTGGATGACAGAA ACCTTGTTGGTC---CAAAATTCGAACCCAGATTGTAAGACAATTTTAAA AGCATTGGGACCAGGGGCTACACTAGAAGAAATGATGACAGCATGTCAGG GAGTGGGAGGACCTGGCCATAAAGCAAGAATTCTGGCTGAGGCAATG--- ---------AGCAAAGCAACA------------------------AGTAC AGCCATAATGATGCAGAAA---AGCAAC---TTTAAGGGC---CAAAAA- --AGAATTGTTAAGTGTTTCAACTGTGGCAAAGAAGGACATATAGCTAGA AATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGG ACACCAAATGAAAGACTGCACT---------GAA---AGGCAGGCTAATT TTTTAGGGAAAATTTGG---CCT---TCCAACAGG---------GGG--- AGGCCAGGAAATTTTCTTCAGAAC-------------------------- ----AGACCA------GAGCCAACAGCC---------------------- -----------------------------CCGCCAGCA---GAGAACTTC GGGTTCGGA---------------GAGGGGATA---ACCCCCTCC----- -------------------CCGAAGCAGGAGCAG---------------- --------AAAGGCGAG---------------------GAACAGGCT--- ---CCTCCC---TTA---GTTTCCCTCAAATCACTCTTTGGCAGCGACCC TTAGTCGCAATAA >Ref.F2.CM.95.95CM_MP257.AJ249237 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCATGGGA AAAAATTCGGTTAAGGCCGGGGGGGAAGAAAAAATATAGGCTGAAACATA TAGTATGGGCAAGCAGGGAGCTAAAACGATTTGCACTTAATCCTGGCCTT TTAGAGACAACAGAAGGCTGTAAGAAAATAATAGGACAACTACAACCATC CCTTCAGACAGGGTCAGAGGAACTGAAATCATTATTTAACACAATAGTAG TTCTCTATTATGTACATCAAAAGATAGAGGTAAGAGACACCAAGGAAGCT TTAGATAAGCTACAGGAAGAACAA------------GAC----------- ----------AAA---------------CATCAG------CAAAAA---- -----------------------------ACACAACAAGCAACGGCT--- ------------------------------GACAAAGGG----------- -------------------------------------------------- -----------------------------GTCAGTAAAGGG--------- ---------GTCAGTCAAAATTACCCTATACTACAAAATCTTCAGGGGCA AATGGTACACCAGAGTCTATCACCTAGAACTTTAAATGCATGGGTAAAAG TAATAGAA---GAGAAGGCTTTCAGCCCAGAAGTAATACCCATGTTTTCA GCATTATCAGAAGGGGCCACCCCACAAGATTTAAACACCATGCTAAACAC AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACCATCAATG AGGAAGCTGCAGAATGGGACAGGTTACATCCAGTGCATGCAGGACCTATC CCACCAGGTCAGATGAGAGAACCAAGGGGAAGTGATATAGCAGGAACCAC TAGTACCCTTCAGGAACAAATAGCATGGATGACA---------AGCAACC CACCTGTC---CCAGTAGGAGAAATCTATAAAAGATGGATAATCCTAGGA TTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAA ACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTCTTTAAAA CTCTAAGAGCTGAGCAAGCCACGCAGGAAGTAAAAGGCTGGATGACAGAA ACCTTGTTGGTC---CAAAATGCGAACCCAGATTGTAAGACCATTTTAAA AGCATTGGGGCCAGGGGCTACACTAGAAGAAATGATGACAGCATGTCAGG GTGTGGGAGGACCTAGCCATAAAGCAAGAATTTTGGCTGAGGCAATG--- ---------AGCAAAGCAACA------------------------GGTGC AGCCATAATGATGCAGAAG---AGCAAC---TTTAAGGGC---CAAAGA- --AGAATTGTTAAGTGTTTTAACTGTGGCAAAGAAGGACATATAGCTAGA AATTGCAGGGCCCCTAGAAAAAGGGGCTGCTGGAAATGTGGACAGGAAGG ACACCAAATGAAAGACTGCACT---------GAG---AGACAGGCTAATT TTTTAGGGAAAATGTGG---CCT---TCCAACAAG---------GGG--- AGGCCCGGAAATTTTCTTCAGAAC-------------------------- ----AGACCA------GAGCCAACAGCC---------------------- -----------------------------CCGCCAGCA---GAGAGCTTC GGGTTCGGG---------------GAGGAGATA---GCTCCCTCC----- -------------------CCGAAGCAGGAGCAG---------------- --------AAAGACAAG---------------------GAACAGGTT--- ---CCTCCC---TTG---ATTTCCCTCAAATCACTCTTTGGCAGCGACCA GTAGTCACAATAA >Ref.F2.CM.97.CM53657.AF377956 ---------AGAGCGTCACTATTAAGCGGGGGAAAATTAGATGATTTGGA AAAAATTCGGTTAAGGCCAGGGGGGAAGAAAAAATATAGGCTGAAACATA TAGTATGGGCAAGCAGGGAGCTAGAAAGATTTGCACTTAATCCTGGCCTT TTAGAGACAAAGGAAGGCTGTAAACAAATAATAGGACAACTACAACCATC CCTTCAGACAGGATCAGAAGAGCTTAAATCATTATTCAACACAATAGTAG TCCTCTATTATGTACATCAAAGGATAAAAATAGGAGACACCAAGGAAGCT TTAGATAAGCTACAGGAAGAACAA------------GAC----------- ----------AAA---------------AGTCAG------CAAAAA---- -----------------------------ACACAACCAGCAGCGGCT--- ------------------------------GACAAAGGG----------- -------------------------------------------------- -------------------------------------------------- ---------GTCAGTCAAAATTACCCTATAGTACAGAATCTTCAGGGACA AATGGTACACCAGTCTCTATCACCTAGAACTTTAAATGCATGGGTAAAAG TAATAGAA---GAGAAGGCTTTCAGCCCAGAAGTAATACCCATGTTTTCA GCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACAC AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACCATCAATG AGGAAGCTGCAGAATGGGACAGATTACATCCAGTGCAGGCAGGACCCATC CCACCAGGTCAGATAAGAGAACCTAGGGGAAGTGATATAGCAGGAACTAC TAGCAACCTACAGGAACAAATAGCATGGATGACA---------AGCAACC CACCTGTC---CCAGTAGGAGAAATCTATAAAAGATGGATAATCCTAGGA TTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAA ACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTCTTTAAAA CTCTAAGAGCTGAGCAAGCTTCACAGGAAGTAAAAGGCTGGATGACAGAC ACCTTGTTGGTC---CAAAATGCGAACCCAGATTGTAAGATCATTTTAAA AGGATTAGGAACAGGGGCTACACTAGAAGAAATGATGACAGCATGTCAGG GGGTGGGGGGACCTGGCCATAAGGCAAGAATTTTGGCTGAGGCAATG--- ---------AGCCAAGTAACA------------------------TCTAC ATCCATATTGATGCAGAAA---AGCAAC---TTTAAGGGC---CAAAGA- --AGAAATGTTAAGTGTTTCAACTGTGGCAAAGAAGGACATATAGCTAAA AATTGCAGGGCCCCTAGAAAAAGGGGCTGTTGGAAATGTGGAAAGGAAGG ACACCAAATGAAAGACTGCACT---------GAG---AGACAGGCTAATT TTTTAGGGAAAATTTGG---CCT---TCCAACAAG---------GGG--- AGGCCTGGAAATTTTCTTCAGAAC-------------------------- ----AGACCA------GAGCCAACAGCC---------------------- -----------------------------CCGCCAGCA---GAAAGCTTC GGGTTCGGA---------------GAAGAGATA---ACTCCCTCC----- -------------------CCGAAGCAGGAGCAG---------------- --------AAAGACAAG---------------------GAAATGTAC--- ---CCTCCC---TTG---ACTTCCCTCAAATCACTCTTTGGCAACGACCC TTAGTCACAATAA >Ref.G.BE.96.DRCBL.AF084936 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCTTGGGA GAAAATTCGGTTGAGGCCAGGGGGAAAGAAAAGATATAGAATGAAACATT TAGTATGGGCAAGCAGGGAGCTGGACAGATTTGCACTTAACCCTGGCCTT TTAGAAACAGCAGAAGGTTGTCAAAAAATAATGGCACAGTTGCAACCAGC TCTCCAAACAGGAACAGAGGAGATTAAATCACTATTTAATACAGTAGCAA CCCTCTATTGTGTACATCAAAAGATAGAGGTAAGAGACACCAAAGAGGCT CTAGAGGAAGTGGAAAAGATACAA------------AAG----------- ----------AAG---------------AGTCAG------CAAAAA---- -------------------------------------------------- ------------------------------GAA---AAC----------- -------------------------------------------------- -----------------------------AGCAGCAGCCAA--------- ---------GTCAGTCAAAATTACCCTATAGTGCAGAATGCACAAGGGCA AATGGTACACCAGGCCATATCACCTAGAACTTTGAATGCATGGGTAAAAG TAGTAGAA---GAAAAGGCCTTCAGTCCAGAAGTAATACCCATGTTTACA GCATTATCAGAAGGAGCCACCCCACAAGATTTAAATACCATGCTAAATAC AGTGGGGGGGCATCAAGCAGCTATGCAAATGTTAAAGGAGACTATCAATG ATGAAGCTGCAGAATGGGACAGGCTACATCCACAGCAGGCAGGGCCTATT GCACCAGGCCAGATAAGGGACCCAACGGGAAGTGATATAGCAGGAGCTAC TAGTACCCTGCAGGAACAGATAAGATGGATGACC---------AGCAACC CACCTGTC---CCAGTGGGAGAAATTTATAAAAGATGGATAATCCTGGGG TTAAATAAAATAGTAAGAATGTACAGCCCTGTCAGCATTTTGGACATAAG ACAGGGGCCAAAAGAACCCTTTAGAGATTATGTGGATAGATTCTTTAAAA CCCTGAGAGCTGAGCAAGCTACACAGGAAGTAAAAAGCTGGATGACAGAC ACCTTGTTGATC---CAAAATGCAAACCCAGATTGTAAGATCATCTTAAA AGGATTAGGACAAGGAGCTACACTAGAAGAAATGATGACAGCATGTCAGG GAGTGGGAGGACCCAGCCATAAAGCAAGAGTTTTAGCTGAGGCAATG--- ---------AGCCAGGCATCAGGTGCA------------------GCAGC AGCCATAATGATGCAGAAA---AGCAAT---TTCAAGGGC---CCAAGA- --AGAACAATTAAATGTTTCAACTGTGGCAAGGAAGGACATCTAGCCAGA AATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAGGG ACATCAAATGAAAGAATGCACA---------GAA---AGACAGGCTAATT TTTTAGGGAAAATTTGG---CCT---TCCAACAAG---------GGG--- AGGCCAGGGAATTTCCTTCAGAAC-------------------------- ----AGGCCA------GAGCCAACAGCC---------------------- -----------------------------CCACCCGCA---GAGAACTTC GGGTTCGGG---------------GAGGAGATA---GCCCCCTCC----- -------------------CCGAAGCAGGAGCAG---------------- --------AAGGAAAAG---------------------GAACTATAT--- ------CCT---CTA---TCTTCCCTCAAATCACTCTTTGGCAACGACCA ATAGTCAAAGTAA >Ref.G.KE.93.HH8793_12_1.AF061641 ATGGGTGCGAGAGCSTCASTATTAAGCGGGGGAAAATTAGATGCATGGGA AAAAATTCGSCTGACGCCAGGGGGAAAGAAAAAATACAGACTGAAACATC TAGTATGGGCAAGCAGAGAGATGGAGAGATTTGCACTTAACCCTGGCCTT TTAGAAACAGCAGAAGGTTGTCAACAAATAATGAGCCAGTTGCAACCAGC TATCCAMACAGGAACAGAGGAGATTAAATCATTATTTAATACAGTAGCAA CCCTCTATTGTGTACATCCCAAGATAGAGGTAAAGGACACCAAAGAAGCT CTAGAGGAAGTAGAAAAGATACAA------------AAG----------- ----------AAA---------------AGTCAG------CAAAAA---- -----------------------------ATACAGCAGGCAGCAAGG--- ------------------------------GATGAAGGA----------- -------------------------------------------------- -----------------------------AACAGCAGCCAA--------- ---------GTCAGCCAAAATTATCCTATAGTGCAGAACGCACAAGGACA GATGGTACACCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAG TAGTAGAA---GAAAAGGCCTTCAGTCCAGAAGTAATACCCATGTTTTCA GCATTATCAGAAGGAGCCACCCCACAAGATTTAAATACCATGCTAAACAC AGTGGGGGGGCATCAAGCAGCTATGCAAATGCTAAAAGATACTATCAATG AGGAAGCTGCAGAGTGGGACAGAATACATCCACCACAGGCAGGGCCTATT CCACCAGGCCAAATAAGAGAACCAAGGGGAAGTGATATAGCAGGAACCAC TAGTAACCTGCAGGAACAAATAAGATGGATGACC---------AGCAACC CACCTATC---CCAGTGGGAGAAATTTATAAAAGATGGATAATCCTGGGA TTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAG ACAAGGGCCAAAAGAACCCTTTAGAGATTATGTAGACAGGTTCTTTAAAA CTTTAAGAGCTGAGCAAGCTACACAGGAAGTAAAAGGCTGGATGACAGAC ACCTTGTTGGTC---CAAAATGCGAACCCAGATTGTAAGACTATCTTAAG AGCATTAGGACCCGGAGCTACACTAGAAGAAATGATGACAGCATGCCAGG GAGTGGGAGGACCCGGCCATAAAGCAAGAGTGTTAGCTGAGGCAATG--- ---------AGCCAGGCAACAGGTGCA------------------GCAGC AGCCATAATGATGCAGAAA---AGCAAC---TTTAAGGGC---CCGAAA- --AGAAATATCAAGTGTTTCAATTGTGGCAAGGAAGGACACTTAGCCAGA AATTGCAGGGCCCCTAGAAAAAAGGGCTGCTGGAAATGTGGAAAGGAGGG ACATCAAATGAAAGACTGCACG---------GAA---AGACAGGCTAATT TTT-AGGGAAAATTTGG---CCT---TCCAACAAG---------GGG--- AGGCCAGGGAATTTTCTTCAGAAC-------------------------- ----AGGCCA------GAGCCAACAGCC---------------------- -----------------------------CCACCCGCA---GAGAGCTTC GGGTTCGGA---------------GAGGAAATA---GCCCCCTCC----- -------------------CCGAAGCCAGAGCCG---------------- --------AAGGAAAAG---------------------GAGATACAT--- ------CCC---TTA---GCTTCCCTCAAATCACTCTTTGGCAGCGACCC CTAGTCACAGTAA >Ref.G.NG.92.92NG083.U88826 GTGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATTCTTGGGA AAAAATTCGGTTAAGGCCAGGGGGAAGGAAAAAGTATAAACTAAAACATA TAGTATGGGCAAGCAGGGAACTGGGGAGATTTGCACTTAACCGTGACCTT TTAGAAACAGCAGAAGGTTGTGTGCAAATAATGAAACAGTTGCAACCAGC TCTCTAGACAGGAACAGAGGAGCTTAGATCATTATTTAATACAGTAGCAA CCCTCTACTGTGTACATCAAAAGATAGAGGTAAAAGACACCAAAGAAGCT CCAGAGGAAGTGGAAAAAATACAA------------AAG----------- ----------AAC---------------AGTCAG------CAAGAA---- -----------------------------ATACAGCAGGCAGCAAAG--- ------------------------------AATGAAGGA----------- -------------------------------------------------- -----------------------------AACAGTAACCCA--------- ---------GTCAGCCAAAATTATCCTATAGTGCAGAATGCACAAGGGCA AATGATACATCAGGCCATATCACCTAGGACTTTGAATGCGTGGGTAAAAG TAGTAGAA---GAAAAGGCCTTCAGTCCAGAAGTAATACCCATGTTTTCA GCATTATCAGAGGGAGCCACCCCACAAGATTTAAATACCATGCTAAATAC AGTGGGGGGGCATCAAGCAGCTATGCAAATGCTAAAGGATACTATCAATG ATGAAGCTGCAGAGTGGGACAGGATACATCCACAGCAGGCAGGGCCTATT CCACCAGGCCAAATAAGAGAGCCTAGTGGAAGTGATATAGCAGGAACTAC TAGTACCCTGCAGGAACAAATAAGATGGATGACC---------AGCAACC CACCTATC---CCAGTGGGAGAAATCTATAAAAGATGGATAATCCTGGGA TTAAATAAAATAGTGAGAATGTATAGCCCTGTCAGCATTTTGGACATAAG ACAAGGGCCAAAAGAACCCTTTAGAGATTATGTAGATAGGTTCTTTAAAA CTTTGAGAGCTGAGCAAGCTACACAGGAAGTAAAAGGTTGGATGACAGAC ACCTTGTTGGTT---CAAAATGCGAACCCAGATTGTAAAACCATCTTAAG AGCATTAGGACCAGGAGCTACACTAGAAGAAATGATGACAGCATGTCAGG GAGTGGGAGGACCCAGCCATAAAGCAAGAGTTTTAGCTGAGGCAATG--- ---------AGCCAGGCATCAGGTGCA------------GCA---GCAGC AGCCATAATGATGCAGAAA---AGCAAT---TTTAAGGGC---CCGAGA- --AGAATTATTAAGTGTTTCAACTGTGGCAAGGAAGGACATCTAGCCAGA AATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAGGG ACATCAAATGAAAGAATGCACG---------GAA---AGGCAGGCTAATT TTTTAGGGAAAATTTGG---CCT---TCCAACAAG---------GGG--- AGGCCAGGAAACTTTCTCCAGAAC-------------------------- ----AGGACA------GAGCCAACAGCC---------------------- -----------------------------CCACCAGCA---GAGAGCTTC GGATTCGGA---------------GAGGAGATA---GCCCCCTCC----- -------------------CCGAAGCAGGAGCCA---------------- --------AAGGAGAAG---------------------GAGCTATAT--- ------CCC---TTA---ACTTCCCTCAAATCACTCTTTGGCAGCGACCC CTAGTCACAGTAA >Ref.G.PT.x.PT2695.AY612637 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCATGGGA AAAAATTCGGTTGAGGCCAGGGGGAAAGAAAAAATATAGAATGAAACATT TAGTATGGGCAAGCAGGGAGCTGGAAAAATTTGCACTCAACCCTGACCTT TTAGAAACAGCAGAAGGTTGTCAACAAATAATGAGACAGTTACAACCAGC TCTCCAGACAGGAACAGAGGAGCTTAGATCATTATTTAATACAGTAGCAA CACTCTATTGTGTACATCAAAGGATAGAGGTAAAAGACACCAAAGAAGCT CTAGAGGAAGTGGAAAAGACACAG------------AAG----------- ----------AAA---------------AGTCAG------AAACAA---- --------------------------------CAGCAGGCAGCAATG--- ------------------------------GACGAAGGA----------- -------------------------------------------------- -----------------------------AACAGCAGCCAA--------- ---------GTCAGCCAAAATTATCCTATAGTGCAGAATGCACAAGGGCA AATGGTACATCAGGCCATATCACCCAGAACTTTAAATGCATGGGTAAAAG TAGTAGAA---GAAAAGGCCTTCAGTCCAGAAGTAATACCCATGTTTTCA GCATTATCAGAAGGAGCCACCCCGCAAGATTTAAATACCATGCTAAACAC AGTAGGGGGGCATCAAGCAGCTATGCAAATGCTAAAGGATACTATTAATG AGGAAGCTGCAGAGTGGGACAGGATACATCCACAACAGGCAGGGCCTATC CCACCAGGCCAGATAAGAGAACCAAGGGGAAGTGATATAGCAGGAACTAC TAGTACCCTGCAGGAACAAATAAGATGGATGACC---------AGCAATC CACCTATC---CCAGTGGGAGAAATTTATAAAAGATGGATAATCCTGGGA TTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGATATAAG ACAAGGGCCAAAAGAACCTTTTAGAGATTATGTAGATAGGTTCTTTAAAA CTTTAAGAGCTGAACAAGCTACACAGGAAGTAAAAGGCTGGATGACAGAC ACCTTGCTGGTC---CAAAATGCGAACCCAGATTGTAAGACCATCTTAAG AGCATTAGGACCAGGAGCTTCACTAGAAGAAATGATGACAGCATGTCAGG GAGTGGGAGGACCCAGTCACAAAGCAAGAGTTTTAGCTGAGGCAATG--- ---------AGCCAGGCATCA------------------------GGGGC AACAATAATGATGCAAAAA---AGCAAC---TTTAAGGGT---CCAAAA- --AGAATGATTAAGTGTTTCAACTGTGGCAAGGAAGGACACCTAGCTAGA AATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAATGTGGAAAGGAGGG ACACCAAATGAAAGACTGCACA---------GAG---AGACAGGCTAATT TTTTAGGGAAAATTTGG---CCT---TCCAACAAG---------GGG--- AGGCCAGGGAATTTTCTCCAGAAC-------------------------- ----AGGCCC------GAGCCAACAGCC---------------------- -----------------------------CCACCCGCA---GAGAGCTTC GGGTTCGGA---------------GAGGAGATA---GCCCCCTCC----- -------------------CCGAAGCAAGAGCCG---------------- --------AAGGACAAG---------------------GAGTTATAC--- ------CCC---TTA---ACCTCCCTCAAATCACTCTTTGGCAGCGACCC CTAGTCACAGTAA >Ref.H.BE.93.VI991.AF190127 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCTTGGGA GAAAATTCGGTTAAGGCCAGGGGGAAGGAAAAAATATAGGCTAAAACATC TGGTATGGGCAAGCAGGGAGCTGGAAAGATTTGCACTTAACCCCGACCTT TTAGAAACAGCAGATGGCTGCCAACAAATACTAGGACAGCTACAGCCAGC TCTTAAGACAGGAACAGAAGACCTTCAATCATTATATAATACAATAGCAG TCCTCTATTGCGTACATCAAAGAATAGATGTGAAAGACACCAAGGAAGCT TTAGGGAAGATAGAGGAAATACAG------------AAT----------- ----------AAG---------------AACAAG------CAAAGA---- -----------------------------ACACAGCAGGCCCCAGCA--- ------------------------GCAGCTGATAAAGAA----------- -------------------------------------------------- -----------------------------AAGGACAGCAAG--------- ---------ATCAGTCAAAATTATCCTATAGTACAGAATGCCCAGGGGCA AATGGTACACCAGGCAATATCACCTAGGACCTTAAATGCATGGGTAAAAG TAGTAGAA---GAGAAGGCTTTTAGCCCAGAAGTAATACCCATGTTTTCA GCATTATCAGAAGGAGCCACCCCACAAGACTTAAATGCCATGCTAAATAC AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACAATCAATG AGGAAGCTGCAGAATGGGATAGGCTACATCCAGTACATGCAGGGCCTATT CCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGATATAGCAGGAACTAC TAGTACCCTTCAGGAACAAGTAGCATGGATGACA---------GGCAATC CCCCAATT---CCAGTGGGAGACATCTATAAGAGATGGATAATCCTGGGA TTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAA ACAAGGACCAAAAGAACCCTTCAGAGACTATGTAGACAGGTTCTTTAGAG TTTTAAGAGCTGAGCAAGCTACACAGGATGTAAAAAACTGGATGACAGAC ACCTTGTTGGTC---CAAAATGCGAATCCAGATTGCAGGACTATTTTAAA AGCATTAGGACGAGGGGCTTCAATAGAAGAAATGATGACAGCATGTCAGG GAGTGGGAGGACCAAGCCATAAAGCAAGAGTTTTGGCTGAGGCAATG--- ---------AGCCAAGTAACAAATGCA------------------AGTGC AGCCATAATGATGCAGAAA---GGCAAC---TTTAAGGGC---CCAAGA- --AGAACTGTTAAATGTTCCAACTGTGGCAAAGAAGGACACATAGCCAGA AATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAATGTGGACAGGAAGG ACACCAGATGAAAGACTGCACA---------GGA---AGACAGGCTAATT TTTTAGGGAAAATTTGG---CCT---TCCAGCAAG---------GGA--- AGGCCAGGGAATTTCCCCCAGAAG-------------------------- ----AGGCTA------GAGCCAACAGCC---------------------- -----------------------------CCACCAGCA---GAGAGCTTC GGGTTCGGA---------------GAGGAGATC---ACCCCCTCT----- -------------------CCGAGGCAGGAGCTG---------------- --------AAAGAACAG---------------------GAACCT------ ------CCT---TTA---ACTTCCCTCAGATCACTCTTTGGCAACGACCA ATAGTCACAGTAA >Ref.H.BE.93.VI997.AF190128 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGACGATTAGATACTTTGGA GAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAGGCTAAAACATA TAGTATGGGCAAGCAGAGAGCTGGAAAGATTTGCACTTAACCCCGGCCTT TTAGAATCAGCAGAAGGCTGTCTACAAATAATAGAACAACTACGGCCATC TATTAAGACAGGAACAGAAGAACTTCWATCATTATTTAATACCGTAGCGA CCCTCTATTGCGTACTTCAAAGAATAGAGGTAAAAGACACCAAGGAAGCT TTAGGGAAGATAGAGGAAATACAA------------AAC----------- ----------AAA---------------AGGCAG------CAAAAA---- -----------------------------ACACAGCAAGCAACAGCT--- ------------------------------AATAAGGAA----------- -------------------------------------------------- -----------------------------AGAGACAACAAG--------- ---------GTCAGTCAAAATTATCCTATAGTACAGAATGCTCAAGGGCA GATGGTACACCAGCCCATATCACVTAGGACCTTAAATGCATGGGTAAAAG TAGTAGAG---GAGAAGGCTTTTAGCCCAGAAGTAATACCCATGTTTTCA GCATTATCAGAAGGAGCCACCCCACAAGACTTAAATGCTATGCTAAATAC AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACAATCAATG AGGAAGCTGCAGAATGGGATAGGCTACATCCAGTGCATGCAGGGCCTATT CCACCAGGCCAGATGAGAGAACCAAGGGGAAGCGATATAGCTGGAACTAC TAGTACCCTTCAGGAACAAATAGCATGGATGACA---------GGCAATC CAAGTATC---CCAGTGGGAGACATCTATAAAAGATGGATAATCCTGGGA TTAAATAAGATAGTAAGAATGTATAGTCCTGTTAGTATTCTGGACATAAA ACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTCTTTAAAA CTTTAAGAGCTGAGCAAGCCACACAGGAGGTGAAGAATTGGATGACAGAC ACCTTGTTGGTC---CAGAATGCAAATCCAGATTGCAAGACTATTTTAAG AGCATTAGGACAAGGGGCTTCAATAGAAGAAATGATGACAGCATGTCAGG GAGTGGGAGGACCTAGTCATAAAGCAAGAGTTTTGGCTGAGGCAATG--- ---------AGCCAAGTAACAAATGCA------------------AATGC AGCCATAATGATGCAGAAA---AGCAAC---TTTAAGGGC---CCAAGA- --AAAATTGTTAAATGTTTCAATTGTGGCAAAGAGGGACACATAGCCAGA AATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAGGGAAGG ACATCAGATGAAGGACTGCACA---------GAG---AGACAGGCTAATT TTTTAGGGAAAATCTGG---CCT---TCCAGCAAA---------GGG--- AGGCCAGGAAATTTTCTCCAGAGC-------------------------- ----AGGCCA------GAGCCAACAGCC---------------------- -----------------------------CCACCAGCA---GAGAGCTTC GGGTTCGGG---------------GAGGAGATG---ACCTCCTCC----- -------------------CCGAAGCAGGAGCTG---------------- --------AAGGACAAG---------------------GAACCT------ ------CCC---TTT---GCTTCCCTCAAATCACTCTTTGGCAACGACCC CTTGTCACAGTAA >Ref.H.CF.90.056.AF005496 ATGGGTGCGAGAGCGTCAGTATTAAGCGGCGGAAAATTAGATGCTTGGGA GAAAATTCGGCTAAGGCCAGGGGGAAAGAAAAAATATAGGCTAAAACATC TAGTATGGGCAAGCAGGGAGCTGGAAAGATTTGCACTTAACCCCGGCCTT TTAGAAACACCAGAAGGCTGTCTACAGATAATAGAACAGATACAGCCAGC TATTAAGACAGGAACAGAAGAACTTAAATCATTATTTAATCTAGTAGCAG TCCTCTATTGCGTACATCGAAAAATAGATGTGAAAGACACCAAGGAGGCT TTAGATAAGATAGAGGAAATACAA------------AAC----------- ----------AAA---------------AGTCAG------CAAAAA---- -----------------------------ACACAGCAAGCAGCAGCT--- ------------------------------GATAAGGAA----------- -------------------------------------------------- -----------------------------AAAGACAACAAG--------- ---------GTCAGTCAAAATTATCCTATAGTACAGAATGCTCAAGGGCA GATGGTACACCAGGCCATATCACCTAGGACCTTAAATGCATGGGTAAAAG TAGTAGAA---GAAAAGGCTTTTAGCCCAGAAGTAATACCCATGTTTTCA GCATTATCAGAAGGAGCCACCCCACAAGACTTAAATGCTATGCTAAATAC AGTGGGGGGACATCAAGCAGCCATGCAGATGTTAAAAGATACAATCAATG AGGAAGCTGCAGAATGGGACAGGGTACATCCAGTGCATGCAGGGCCTATT CCACCAGGCCAAATGAGAGAACCAAGGGGAAGCGATATAGCAGGAACTAC TAGTACCCTGCAGGAACAAATAGCATGGATGACA---------GGCAATC CAGCTATC---CCAGTGGGAGACATCTATAAAAGATGGATAATCCTGGGA TTAAATAAGATAGTAAGAATGTATAGTCCTGTCAGCATTCTGGACATAAA ACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTTTTTAAAA CTTTAAGAGCTGAGCAAGCCACACAGGATGTGAAGAATTGGATGACAGAA ACCTTGTTGGTC---CAAAATGCAAATCCAGATTGCAAGACTATATTAAG AGCATTAGGACAAGGGGCTTCAATAGAAGAAATGATGACAGCATGTCAGG GAGTGGGAGGACCTAGTCATAAAGCAAGAGTTTTGGCTGAGGCAATG--- ---------AGCCAAGTAACAAATACA------------------AATAC AGCCATAATGATGCAGAAA---GGCAAC---TTTAAGGGC---CAAAGA- --AAATTTGTTAAATGCTTCAACTGTGGCAAAGAGGGACACATAGCCAGA AATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAGAGAAGG ACATCAGATGAAAGACTGCACA---------GAG---AGACAGGCTAATT TTTTAGGGAAAATTTGG---CCT---TCCAGCAAA---------GGG--- AGGCCAGGAAATTTTCTCCAGAGC-------------------------- ----AGGCCA------GAACCAACAGCC---------------------- -----------------------------CCACCAGCA---GAGAGCTTC GGGTTCGGA---------------GAGGAGATG---ACCCCCTCT----- -------------------CCGAAGCAGGAGCAG---------------- -----CTGAAGGACAAG---------------------GAACCT------ ------CCC---TTA---GCTTCCCTCAGATCACTCTTTGGCAGCGACCC CTTGTTACAGTAA >Ref.H.GB.00.00GBAC4001.FJ711703 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCTTGGGA GAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAGGCTAAAACATC TAGTATGGGCAAGCAGGGAGCTGGACAGATTTGCACTCAACCCCGACCTT TTAGAAACAGCAGATGGCTGTCTAAAAATAYTAGGACAGATACAGCCAGC TCTTCAGACAGGAACAGAAGAAATTAAATCGTTATTTAATCTAGTAGCAG TCCTCTATTGTGTACATCAGAAAATAGAGGTACAAGATACCAGTGAAGCT TTAAATAAGGTAAAGGAGATACAG------------AAC----------- ----------AAG---------------AACCAG------CAAACA---- -----------------------------ACACAGCAGGCAACAGCT--- ------------------------------RGTAAAGAG----------- -------------------------------------------------- -----------------------------AAGGACAGCAAG--------- ---------ATCAGTCAAAATTATCCTATAGTACAGAATGCCCAAGGGCA AATGGTACACCAGGCCATATCACCTAGGACCTTAAATGCATGGGTAAAAG TAGTAGAA---GAGAAGGCTTTTAGCCCAGAAGTAATACCCATGTTTTCA GCATTATCAGARGGAGCMACCCCACAAGACYTAAATACCATGTTAAACTC AGTGGGGGGACATCAGGCAGCCATGCAAATRTTAAAAGATACAATCAATG AGGAAGCTGCAGAATGGGATAGGACACATCCAGTGCATGCAGGGCCTATT CCACCAGGCCAGATGAGAGAACCAAGGGGAAGCGATATAGCAGGAACTAC TAGYAACCTTCAGGAACAAATAGCATGGATGACA---------RGYAATC CCCCTRTC---CCAGTGGGRGAKATCTATAAAAGATGGATAATCWTGGGA TTAAATAAAATAGTAAGAATGTATAGTCCTGTCAGCATTTTGGACATAAA ACAAGGGCCAAAAGAACCCTTTAGAGAYTATGTAGACAGGTTYTTTAAAA CTTTAAGAGCTGAGCAAGCCACACAGGACGTGAAGAATTGGATGACAGAC ACCTTGTTGGTC---CAAAATGCAAATCCAGATTGCAAGACTATTTTAAA AGCATTAGGACAAGGGGCTTCAATAGAAGAAATGATGACAGCATGTCAGG GAGTGGGAGGACCTGGCCATAAAGCAAGAGTTTTGGCTGAGGCAATG--- ---------AGTCAAATGACAAATATG------------------AATAC AGCCATAATGGTGCAGAAA---GGCAAC---TTTAAGGGC---CAAAGA- --AGAACTGTTAAATGTTTCAACTGTGGTAAAGAAGGACACATAGCAAGA AACTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGGAGGGAAGG ACATCAGATGAAAGACTGCACA---------GAG---AGACAGGCGAATT TTTTAGGGAAAATCTGG---CCT---TCCAGCAAA---------GGG--- AGGCCAGGGAACTTTCTCCAGAGC-------------------------- ----AGGCCA------GAACCAACAGCC---------------------- -----------------------------CCACCAGCA---GAATGCTTC GGGTTCGGG---------------GAGGAGATG---ACACCCCCT----- -------------------CCGAAGCAGGAGATG---------------- --------AAGGAAAAG---------------------GAACCT------ ------CCC---TTA---ACTTCCCTCAGATCACTCTTTGGCAGCGACCC CTTGTCACAGTAA >Ref.J.CD.97.J_97DC_KTB147.EF614151 ------------------------------------------GCATGGGA GAAAATTTGGCTGAGGCGACGGGGAGAGAAAAAATACAGGCGAAAACATA TAGTATGGGCAAGCAGGGAGCTGGACAGATATGCACTTAACCCTGGCCTT CTATAGTGAGCAGAAGGCGGTGAACAGATACTAGTACAGATCCAACCAGA TCTTTAAACAGGAGCAGAGGAGATAAAATCATTATTTAACACAGAAGCAA CCCTCTATTGTGTACATTAGAGGATAGACATAAGAGACACCAAGGAGGCT TTAGACAAGATAGAGGAACTTTAA------------AAC----------- ----------AAA---------------AGCAAG------GAGAAA---- -----------------------------GCTAAGAAAGAA---GCT--- ------------------------------GTCAAAAAA----------- -------------------------------------------------- -----------------------------TACAACAGTCAG--------- ---------GTGAGTCACAATTATCCTATATTGCAAAATATGTAAGGGGA ACTAGTACACCAGGCCCTATCACCTAGAACATTAAATGCATGGGTAAAGG TGATAGAA---GAGAAAGGTTTCAACCCAGAAGTGATACCCATGTTTTCA GCATTATCAGAAGGAGCCACTCCACAAGATTTAAATACCATGCTAAACAC GGTGGGGGGACATCAAGCAGCGATGCAAATGTTAAAAGATACCATCAATG AGGAAGCTGCAGAATGGGACAGGCTCCATCCAGTACATGCAGGACCTGTT GCACCAGGTCAGATGAGAGAACCGAGGGGAAGTGATATAGCAGGAACTAC TAGTAACCTTCAGGAACAAATAGCATGGATAACAGGCAACGGTGGCAACC AACCTATC---CCAGTAGGAGAAATCTATAAAAGATGGATAATTTTAGGA TTAAATAAAATAGTGAGAATGTATAGCCCTGTCAGCATTTTGGACATAAG GCAAGGACCAAAAGAACCTTTTAGAGACTATGTGGATAGGTTCTTTAAAA CTCTAAGAGCCGAGCAAGCTACACAGGAGGTAAAAAATTGGATGACAGAT ACCTTGTTGGTC---CAAAATGCGAATCCAGATTGTAAGACCATTCTAAG AGCATTAGGAGCAGGAGCTACACTAGAAGAAATGATGACAGCATGTCAGG GAGTGAGAGTATCCAGTCATAGAGCAAGAGTTTTTGGTGAGGCAATA--- ---------AGCCAAGTAAAC------------------------AATAC AAACATAATAATGCAAAGA---GGTAAC---TTTAGGGGC---CAGAAG- --AGAAGTGTTAAATGTTTCAACTGTGGTAAAGAGGGACACATAGCAAAA AATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGAAAGTGTGGAAAGGAAGG ACACCAAATAAAAAACTGCACT---------GAG---AGACAGGCCAATT TTTTAGGGAAAGTTTGG---CCT---TCCAGCAAG---------GGG--- AGGCCAGGGAACTTTCTCCAGAGC-------------------------- ----AGGCCA------GAACCAACAGCC---------------------- -----------------------------CCACCAGCA---GAAAGCTTC GGGTTCGGG---------------GAGAAGATA---ACTCCCTCC----- -------------------CAGAAACAGGAACCG---------------- --------AGGAAG------------------------GAACTATAT--- ------CCT---TCA---GCTTCCCTCAAATCACTCTTTGGCAGCGACCC CTCGTCACAGTAA >Ref.J.CM.04.04CMU11421.GU237072 ATGGGTGCGAGAGCGTCAGTATTAAGCGGCGGAAAATTAGATACTTGGGA GAAAATTCGGTTGAGGCCAGGGGGGAAGAAACGTTATAGGCTAAAACATT TAGTATGGGCAAGCAGGGAGCTGGACAGATTTGCACTTAACCCTGRCCTT CTAGAAACATCAAAAGGCTGTCAACAAATATTAGTACAGCTCCAACCATC TTATCAAACAGGGACAGAAGAAATTAAGTCATTATATAACACAGTAGCAA CCCTCTATTGCGTACATGAGGRSATAGAGGTAAAAGACACCAAGGAARCT TTAGACAAGATAGAGGAACTACAA------------AAG----------- ----------AAG---------------AACAAG------CAACAG---- -----------------------------GCACAGAAAGCAGAARCT--- ------------------------------GACAAAAGR----------- -------------------------------------------------- -----------------------------RACARCAGTCAA--------- ---------GTCAGTCAAAATTATCCTATAGTGCAGAACATGCAAGGGCA ACCAGTACAYCARGCCCTATCACCTAGAACTTTAAATGCATGGGTAAAAG TGRTAGAA---GARAAGGCTTTYAGCCCAGAAGTAATACCCATGTTTTCA GCYTTATCAGAAGGAGCCACCCCRCAAGATTTAAATACCATGCTAAATAC AGTRGGGGGACACCARGCAGCTATGCAAATGTTAAAAGATACTATCAATG AGGAAGCTGCAGAATGGGATAGGKTACATCCAGTACATGCAGGGCCTCCR GCACCAGGCCAGGCGAGAGAACCGAGGGGAAGTGATATAGCAGGAACTAC TAGTACCCTCCAGGAACAAATAGCATGGATGACA---------GGCAACC CACCTATC---CCAGTAGGGGAAATTTATAAAAGRTGGATAATTCTGGGA TTAAATAAAATAGTRAGAATGTATAGCCCTGTCAGCATTTTGGATATAAG ACAAGGACCAAAAGARCCTTTTAGAGAYTATGTAGATCGGTTCTTTAAAA CTCTAAGAGCTGAGCAAGCTACACAGGAAGTAAAAAATTGGATGACAGAT ACCTTGTTGATC---CAAAATGCAAATCCAGATTGCAGAACCATYTTAAA AGCATTAGGACCAGGAGCTACACTAGARGAAATGATGACAGCATGYCAGG GAGTGGGAGGACCTGGTCATAAAGCAAGAGTTTTGGCWGAAGCAATG--- ---------AGCCAAATGACCAAT---------------------ACAGC AAACATAATGATGCAAARG---GGTAAY---TTTAAGGGC---CARAAA- --AGAATGATTAAGTGTTTCAATTGTGGWAAACCAGGACACCTAGCMAGA AAYTGCAGAGCCCCTAGRAARAAGGGCTGTTGGAAATGTGGACAGGAAGG ACAYCAAATGAAAGACTGCACT---------GAG---AGACAGGCTAATT TTTTAGGGAARATCTGG---CCT---TCCAACAAR---------GGG--- AGGCCAGGGAACTTTCTYCAGAGC-------------------------- ----AGRCCA------GAGCCAACAGCC---------------------- -----------------------------CCACCAGCA---GAGAGCTTC GGGTTCGGG---------------GAAGAGACC------YCYYCC----- -------------------CCGAAACAAGAAGCG---------------- --------AAG---------------------------GAACTGTAT--- ------CCT---CTA---ACTTCCCTCAAATCACTCTTTGGCARCGACCC CTYGTCACAATAA >Ref.J.SE.93.SE9280_7887.AF082394 ATGGGTGCGAGAGCGTCAATATTAAGTGGGGGAAAATTAGATGATTGGGA AAAAATTCGGTTGAGGCCAGGGGGGAAGAAAAAATATAGGATAAAGCATC TAGTATGGGCAAGCAGGGAGCTGGACAGATTTGCACTTAACCCTGGCCTT CTAGAGTCAGCAAAAGGCTGTCAACAAATACTAGTACAGCTCCAACCAGC TCTCCAGACAGGAACACAAGAAATTAAATCATTGTATAATACAGTAGCAA CCCTCTATTGCGTACATCAGAGGATAGAAATAAAAGACACCATGGAAGCT TTAGAGAAGATAGAGGAAATTCAA------------AAC----------- ----------AAG---------------AACAAA------CAGCAG---- -----------------------------GCACAGAAAGCAGAAACT--- ------------------------------GACAAAAAA----------- -------------------------------------------------- -----------------------------GACAACAGTCAG--------- ---------GTCAGTCAAAATTATCCTATAGTGCAGAATCTGCAAGGGCA ACCGGTACACCAGGCCCTATCACCTAGAACTTTAAATGCATGGGTAAAAG TGATAGAA---GAAAAAGCTTTCAGCCCAGAAGTGATACCCATGTTTTCA GCATTATCAGAAGGAGCCACCCCGCAAGATTTAAATACCATGCTAAACAC AATAGGGGGACACCAAGCAGCTATGCAAATGTTAAAAGATACTATCAATG AGGAAGCTGCAGAATGGGACAGGGTACATCCAGTACATGCAGGGCCTATT GCACCAGGCCAGGTGAGAGAACCAAGGGGAAGTGATATAGCAGGAACTAC TAGTACCCTCCAGGAACAAATAGGATGGATGACA---------GGCAATC CACCTATC---CCAGTAGGAGAGATTTATAAAAGATGGATAATTCTGGGA CTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGTATTTTGGATATAAG ACAAGGACCAAAAGAACCTTTTAGAGACTATGTAGACAGGTTCTTTAAAG CTCTAAGAGCTGAGCAAGCTACACAGGATGTAAAAAATTGGATGACAGAT ACCTTGCTGGTC---CAAAATGCAAATCCAGATTGCAAGACCATTTTAAA AGCATTAGGATCAGGAGCTACACTAGAAGAAATGATGACAGCATGTCAGG GAGTGGGAGGACCTGGTCATAAGGCGAGAGTTTTGGCTGAAGCAATG--- ---------AGCCAAGTGACC------------------------AATAC CAACATAATGATGCAAAGA---GGTAAC---TTTAGGGAC---CATAAA- --AGAATTGTTAAGTGTTTCAATTGTGGCAAACAAGGACACATAGCAAAA AACTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGG ACACCAAATGAAAGACTGCACT---------GAG---AGACAGGCTAATT TTTTAGGGAAGATTTGG---CCT---TCCAGCAAA---------GGG--- AGGCCAGGGAACTTTCTCCAGAGC-------------------------- ----AGACCA------GAGCCAACAGCC---------------------- -----------------------------CCACCAGCA---GAGAGCCTC GGGCTCGGA---------------GAGGAGATC------CCCTCC----- -------------------CCGAAACAGGAGCCG---------------- --------AAGGACAAG---------------------GAACTGTAT--- ------CCT---CTA---ACTTCCCTCAAATCACTCTTTGGCAGCGACCC CTTGTCACAATAA >Ref.K.CD.97.97ZR_EQTB11.AJ249235 ATGGGTGCGAGAGCTTCAGTATTAAGCGGGGGAAAATTAGACAAATGGGA AAAAATTCAGTTACGGCCAGGGGGAAAGAAAAAATACAGGCTAAAACATC TAGTATGGGCAAGCAGGGAGCTAGAACGATTTGCACTTAACCCTAACCTT TTAGAGACAGTAGAAGGCTGTCGGCAAATAATAAGACAACTACAACCATC CCTTCAAACAGGCTCGGAAGAGCTTAGATCACTATTTAATACAGTAGCAA CCCTCTATTGGGTGCATCAAAGTATACAGGTAAGGGACACCAAGGAAGCC TTAGACAAACTAGAGGAAGAACAA------------AAC----------- ----------AGA---------------ACTCAG------CAAAAG---- -----------------------------ACACAGCAAGGAAAAGCT--- ------------------------------GACAAAGGG----------- -------------------------------------------------- -------------------------------------------------- ---------GTTAGTCAAAATTACCCTATAGTACAGAATCTTCAGGGGCA AATGGTACACCAGGCCCTATCACCTAGAACTTTAAATGCATGGGTTAAAG TAATAGAA---GAGAAGGCTTTCAGCCCAGAAGTAATACCCATGTTTTCA GCATTATCAGAAGGAGCCACTCCACAAGATTTAAACACCATGCTAAACAC AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACTATCAATG AGGAAGCTGCAGAATGGGACAGGATGCACCCAGTGCAAGCAGGGCCTATC CCACCAGGCCAAATAAGAGAACCTAGGGGGAGTGATATAGCAGGAACTAC TAGCACTCTTCAGGAACAAATAACATGGATGACA---------AGCAACC CACCTATC---CCAGTGGGAGAAATCTATAAAAGATGGATAATCCTGGGG TTAAATAAAATAGTGAGAATGTATAGCCCTGTCAGCATTTTGGACATAAG ACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGATAGGTTCTTTAGAG TTCTAAGAGCTGAACAAGCCACACAGGAAGTAAAAAATTGGATGACAGAA ACCCTGTTGGTC---CAAAACGCAAACCCAGATTGTAGGACCATTTTAAA GGCGTTGGGATCAGGGGCTACATTAGAAGAAATGATGACAGCATGTCAGG GAGTAGGAGGGCCTGGCCATAAAGCAAGGGTTTTGGCTGAGGCAATG--- ---------AGCCAGGTAACA------------------------AATTC AGCCGTAATGATGCAGAGA---GGCAAC---TTTAAGGGT---CAAAGA- --AGAATTATTAAGTGCTTCAACTGTGGCAAAGAAGGACACCTAGCCAGA AATTGTAGGGCCCCTAGAAAAAAGGGCTGTTGGAAATGTGGGAAAGAAGG ACATCAGATGAAAGACTGTTCT---------GAG---AGACAGGCTAATT TTTTAGGGAAGTTCTGG---CCT---CTCAACAAA---------GAG--- AGGCCAGGAAATTTTCTTCAGAAC-------------------------- ----AGACCA------GAGCCAACAGCC---------------------- -----------------------------CCACCAGCA---GAGAGCTTT GGGTTCGGG---------------GAGAAGATA---ACCCCCTCT----- -------------------CTGAGACAGGAAATG---------------- --------AAAGATCAG---------------------GAACAGGGT--- ---CCTCCT---TTA---ACTTCCCTCAAATCACTCTTTGGCAGCGACCC GTTGTCACAGTAA >Ref.K.CM.96.96CM_MP535.AJ249239 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCATGGGA AAAGATTCGGTTACGGCCAGGGGGAAAGAAAAAATATAAACTGAAACATC TAGTATGGGCAAGCAGGGAGCTAGAACGATTTGCACTCAACCCTGGCCTT TTAGAGACAACAGAAGGCTGTCGGCAAATAATAACACAAATACAGCCATC CATTCAAACAGGATCAGAAGAGATTAAATCACTATATAATACAATAGCAG TCCTCTATTTTGTACATCAAAAGATAGAGGTAAAAGACACCAAGGAAGCC TTAGACAAACTAGAGGAAGAACAA------------AAC----------- ----------AAA---------------AGTCAG------CGAAAG---- -----------------------------ACACAACAAGAAGCAGCT--- ------------------------------GACAAAGGG----------- -------------------------------------------------- -------------------------------------------------- ---------GTCAGTCAAAATTACCCTATAGTACAGAATCTGCAGGGGCA AATGGTACACCAGGCCCTATCACCTAGAACTTTAAATGCATGGGTGAAGG TAATAGAG---GAGAAGGCTTTCAGCCCAGAAGTAATACCCATGTTTACA GCATTATCAGAAGGAGCCACTCCACAAGATCTAAACACCATGCTAAACAC AGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACTATCAATG ATGAAGCTGCAGAATGGGACAGGTTACACCCAGTGCATGCAGGGCCTATC CCACCAGGCCAAATGAGAGAACCGAGGGGGAGTGACATAGCAGGAACTAC CAGCACCCTTCAGGAACAAATAGCATGGATGACA---------AGCAACC CACCTGTC---CCAGTGGGGGAAATCTATAAAAGATGGATAATCCTGGGT TTAAACAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAG ACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGATAGGTTCTTTAAAA CCCTAAGAGCTGAACAAGCCACACAGGAAGTAAAGAATTGGATGACAGAC ACCCTGTTGGTC---CAAAACGCAAACCCAGATTGTAAGACCATTTTAAA AGCGTTGGGACCAGGGGCTTCATTAGAAGAGATGATGACAGCATGTCAGG GAGTGGGAGGGCCTAGCCATAAAGCAAGAATTTTGGCTGAGGCAATG--- ---------AGCCAGGTAACA------------------------AATCC AGTTGTAATGATGCAGAAA---GGCAAC---TTTAAGGGC---CATAGA- --AAAATTGTTAAGTGCTTCAACTGTGGCAAAGAAGGGCACATAGCCAGA AATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAATGTGGGAAGGAAGG ACATCAGATGAAAGACTGCACT---------GAG---AGACAGGCTAATT TTTTAGGGAAAATCTGG---CCT---TCCCACAAG---------GGG--- AGGCCAGGGAATTTTCTTCAGAGC-------------------------- ----AGACCA------GAGCCAACAGCC---------------------- -----------------------------CCACCAGCA---GAGAGCTTC GGGTTCGGG---------------GAGGAGATA---ACCCCCTCT----- -------------------CCGAGGCAGGAGACC---------------- --------AAAGACAAG---------------------GAACAGAGC--- ---CCTCCT---TTA---ACTTCCCTCAAATCACTCTTTGGCAACGACCC ATTGTCACAATAA bppsuite-2.4.1/Examples/Data/HIV1_REF_2010_gag_macse_AA.fasta000066400000000000000000000551011333524216000232150ustar00rootroot00000000000000>Ref.D.CD.83.ELI.K03454 MGARASVLSGGKLDKWEKIRLRPGGKKKYRLKHIVWASRELERYALNPGLLET-SEGCKQIIGQLQP-AIQTGTEELRSLYNTVATLYCVH-KGIDVKDTKEALEKMEEE-QNKSK---KKAQQA--AADTGNNS------QVSQNYPIVQNLQ-GQMVHQAISPRTLNAWVKVIEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIAWMTSN---PPIPVGEIYKRWIIVGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFYKTLRAEQASQDVKNWMTETLLVQNANPDCKTILKALGPQATLEEMMTACQGVGGPSHKARVLAEAMS--QA--T---NSVTT---AMMQRGNFKGPRKIIKCFNCGKEGHIAKNCRAPRKKGCWR-CGKEGHQLKDCTERQANFLGRIWPSHKGRPGNFLQSRP----------EPTAPPA-----------ESFGFGEEIT-PSQKQEQ-KD--KEL---YPLTSLKSLFGNDPLSQ*- >Ref.C.ET.86.ETH2220.U46016 MGARASILRGEKLDAWEKIKLRPGGKKHYMLKHLVWANRELEKFALNPDLLDT-SAGCKQIIKQLQP-ALQTGTEELKSLFNTVATLYCVH-QKIEIKDTKEALDKIEEE-QNESQ---QKTQQA-GAADRG---------KDSQNYPIVQNMQ-GQMVHQPISARTLNAWVKVVEEKAFSPEVIPMFTALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPVAPGQMRDPRGSDIAGTTSTLQEQIAWMTGN---PPVPVGDIYKRWIILGLNKIVRMYSPVSILDIKQGPKEPFRDYVDRFFKTLRAEQATQDVKNWMTDTLLVQNANPDCKTILRALGPGASLEEMMTACQGVGGPAHKARVLAEAMS--QV--N---N--TT---IMMQKSNFKGPKRAIKCFNCGKEGHLARNCRAPRKKGCWK-CGKEGHQMKDCTERQANFLGRLWPSNKGRPGNFLQSRP----------EPTAPPESLRPEPTAPPPESFRF-EEAT-PSPKQEL-KD--RE-----ALTSLKSLFGNDHLLQ*- >Ref.C.ZA.04.04ZASK146.AY772699 MGARASVLRGEKLDTWEKIRLRPGGKKHYMLKHIVWASRELERFALNPGLLET-SEGCKQILAQIQP-AIQTGTEELKSLFNTIAVLYCVH-KKIDVRDTKEALDKIEEE-QNKSQ---QKTQQA-KAADE----------KVSQNFPIVQNLQ-GQMVHQPLSPRTLNAWVKVIEEKGFNPEVIPMFTALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPVAPGQMREPRGSDIAGTTSNLQEQVAWMTSN---PPIPVGDIYKRWIILGLNKIVRMYSPVSILDIKQGPKEPFRDYVDRFFKTLRAEQATQEVKNWMTDTLLVQNANPDCKTILRALGPGATLEEMMAACQGVGGPGHKARVLAEAMS--QI--N---N--GN---IMMQRSNFKGPKRIVKCFNCGKGRHIAKNCRAPRKKGCWK-CGKEGHQMKDCTERQANFLGKIWPSQKGRPGNFLQNRL----------EPTAPPA-----------ESFRF-EETT-PAPKQEL-KD--RE-----PLTSLRSLFGSDPLSQ*- >Ref.A1.UG.92.92UG037.AB253429 MGARASVLSGGKLDAWEKIRLRPGGKKKYRLKHLVWASRELERFALNPSLLET-TEGCQQIMEQLQS-ALRTGTEELRSLYNTVATLYCVH-QRIEVKDTKEALDKIEEI-QKKSK---QKTQQA--AADTGSSS------KVSQNYPIVQNAQ-GQMIHQSLSPRTLNAWVKVIEEKAFSPEVIPMFSALSEGATPQDLNMMLNIVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPVAPGQMREPRGSDIAGTTSTPQEQIAWMTGN---PPIPVGDIYKRWIILGLNKIVRMYSPVSILDIKQGPKEPFRDYVDRFFKTLRAEQATQEVKGWMTETLLIQNANPDCKSILRALGAGATLEEMMTACQGVGGPGHKARVLAEAMS--QV--Q---H--TN---IMMQRGNFKGQKR-IKCFNCGKEGHLAKNCRAPRKKGCWK-CGREGHQMKDCTERQANFLGKIWPSSKGRPGNFPQSRP----------EPTAPPAA----------EIFGMREEIV-SPPKQEQ-ND--RDQ--NPPSVSLKSLFGNDLLSQ*- >Ref.A1.RW.92.92RW008.AB253421 MGARASVLSGGKLDAWEKIRLRPGGKKKYRMKHLVWASRELERFALNPGLLET-TEGCQKIIEQLQP-SVKTGTEELKSLFNTVATLYCVH-QRIDVKDTKEALDKIEEM-QNKSK---QKTQQA--AADIGNSS------KVSQNYPIVQNAQ-GQMIYQSMSPRTLNAWVKVIEEKGFNPEVIPMFSALSEGATPQDLNMMLNIVGGHQAAMQMLKDTINEEAADWDRLHPVQAGPIPPGQMREPRGSDIAGTTSTPQEQIGWMTSN---PPIPVGDIYKRWIILGLNKIVRMYSPVSILDVKQGPKEPFRDYVDRFFKILRAEQATQDVKHWMTETLLIQNANPDCKSILRALGTGATLEEMMTACQGVGGPSHKARVLAEAMS--QV--Q---H--PN---IMMQRGNFRGQKR-IKCFNCGKEGHLARNCRAPRKKGCWK-CGKEGHQMKDCTERQANFLGKIWPSSKGRPGNFPQSRP----------EPSAPPA-----------EIFGIGEEIA-SPPKQEQ-KD--REP--AQPLVSLKSLFGNDPLSQ*- >Ref.H.BE.93.VI997.AF190128 MGARASVLSGGRLDTLEKIRLRPGGKKKYRLKHIVWASRELERFALNPGLLES-AEGCLQIIEQLRP-SIKTGTEEL?SLFNTVATLYCVL-QRIEVKDTKEALGKIEEI-QNKRQ---QKTQQA--TANKERDN------KVSQNYPIVQNAQ-GQMVHQPIS?RTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNAMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPIPPGQMREPRGSDIAGTTSTLQEQIAWMTGN---PSIPVGDIYKRWIILGLNKIVRMYSPVSILDIKQGPKEPFRDYVDRFFKTLRAEQATQEVKNWMTDTLLVQNANPDCKTILRALGQGASIEEMMTACQGVGGPSHKARVLAEAMS--QV--T---N--ANA-AIMMQKSNFKGPRKIVKCFNCGKEGHIARNCRAPRKKGCWK-CGREGHQMKDCTERQANFLGKIWPSSKGRPGNFLQSRP----------EPTAPPA-----------ESFGFGEEMT-SSPKQEL-KD--KE----PPFASLKSLFGNDPLSQ*- >Ref.H.BE.93.VI991.AF190127 MGARASVLSGGKLDAWEKIRLRPGGRKKYRLKHLVWASRELERFALNPDLLET-ADGCQQILGQLQP-ALKTGTEDLQSLYNTIAVLYCVH-QRIDVKDTKEALGKIEEI-QNKNK---QRTQQAPAAADKEKDS------KISQNYPIVQNAQ-GQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNAMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPIPPGQMREPRGSDIAGTTSTLQEQVAWMTGN---PPIPVGDIYKRWIILGLNKIVRMYSPVSILDIKQGPKEPFRDYVDRFFRVLRAEQATQDVKNWMTDTLLVQNANPDCRTILKALGRGASIEEMMTACQGVGGPSHKARVLAEAMS--QV--T---N--ASA-AIMMQKGNFKGPRRTVKCSNCGKEGHIARNCRAPRKKGCWK-CGQEGHQMKDCTGRQANFLGKIWPSSKGRPGNFPQKRL----------EPTAPPA-----------ESFGFGEEIT-PSPRQEL-KE--QE----PPLTSLRSLFGN!PIVTV! >Ref.G.PT.x.PT2695.AY612637 MGARASVLSGGKLDAWEKIRLRPGGKKKYRMKHLVWASRELEKFALNPDLLET-AEGCQQIMRQLQP-ALQTGTEELRSLFNTVATLYCVH-QRIEVKDTKEALEEVEKT-QKKS----QKQQQA--AMDEGNSS------QVSQNYPIVQNAQ-GQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRIHPQQAGPIPPGQIREPRGSDIAGTTSTLQEQIRWMTSN---PPIPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFKTLRAEQATQEVKGWMTDTLLVQNANPDCKTILRALGPGASLEEMMTACQGVGGPSHKARVLAEAMS--QA--S---G--AT---IMMQKSNFKGPKRMIKCFNCGKEGHLARNCRAPRKKGCWK-CGKEGHQMKDCTERQANFLGKIWPSNKGRPGNFLQNRP----------EPTAPPA-----------ESFGFGEEIA-PSPKQEP-KD--KEL---YPLTSLKSLFGSDP!VTV! >Ref.K.CM.96.96CM_MP535.AJ249239 MGARASVLSGGKLDAWEKIRLRPGGKKKYKLKHLVWASRELERFALNPGLLET-TEGCRQIITQIQP-SIQTGSEEIKSLYNTIAVLYFVH-QKIEVKDTKEALDKLEEE-QNKSQ---RKTQQE--AADKG----------VSQNYPIVQNLQ-GQMVHQALSPRTLNAWVKVIEEKAFSPEVIPMFTALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINDEAAEWDRLHPVHAGPIPPGQMREPRGSDIAGTTSTLQEQIAWMTSN---PPVPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFKTLRAEQATQEVKNWMTDTLLVQNANPDCKTILKALGPGASLEEMMTACQGVGGPSHKARILAEAMS--QV--T---N--PV---VMMQKGNFKGHRKIVKCFNCGKEGHIARNCRAPRKKGCWK-CGKEGHQMKDCTERQANFLGKIWPSHKGRPGNFLQSRP----------EPTAPPA-----------ESFGFGEEIT-PSPRQET-KD--KEQ--SPPLTSLKSLFGNDPLSQ*- >Ref.F2.CM.97.CM53657.AF377956 ---RASLLSGGKLDDLEKIRLRPGGKKKYRLKHIVWASRELERFALNPGLLETK-EGCKQIIGQLQP-SLQTGSEELKSLFNTIVVLYYVH-QRIKIGDTKEALDKLQEE-QDKSQ---QKTQPA--AADKG----------VSQNYPIVQNLQ-GQMVHQSLSPRTLNAWVKVIEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVQAGPIPPGQIREPRGSDIAGTTSNLQEQIAWMTSN---PPVPVGEIYKRWIILGLNKIVRMYSPVSILDIKQGPKEPFRDYVDRFFKTLRAEQASQEVKGWMTDTLLVQNANPDCKIILKGLGTGATLEEMMTACQGVGGPGHKARILAEAMS--QV--T---S--TS---ILMQKSNFKGQRRNVKCFNCGKEGHIAKNCRAPRKRGCWK-CGKEGHQMKDCTERQANFLGKIWPSNKGRPGNFLQNRP----------EPTAPPA-----------ESFGFGEEIT-PSPKQEQ-KD--KEM--YPPLTSLKSLFGNDP!VTI! >Ref.F1.FI.93.FIN9363.AF075703 MGARASVLSGGKLDAWEKIRLRPGGKKQYRIKHLVWASRELERFAIDPGLLET-SEGCQKIIAQIQP-SIQTGSEELRSLYNTIAVLYFVH-QKIEVKDTKEALDKLEEE-QNKSQ---QKTQQAAAAADKG----------VSQNYPIVQNLQ-GQMVHQAISPRTLNAWVKVIEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPIPPGQMREPRGSDIAGTTSTLQEQIQWMTSN---PPVPVGDIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFKALRAEQATQEVKGWMTDTLLVQNANPDCKIILKGLGIGATLEEMMTACRGVGGPGHKARILAEAMS--QA------N--TT---IMMQKSNFRGQRRIVKCFNCGKEGHIARNCRAPRKKGCWK-CGQEGHQMKDCTERQANFLGKIWPSNKGRPGNFLQSRP----------EPTAPPA-----------ESLGIREEVT-PSPRQEQ-KE--EGQ--YPPLASLKSLFGNDP!VTI! >Ref.D.UG.94.94UG114.U88824 MGARASVLSGGKLDEWEKIRLRPGGKKKYRLKHLVWASRELERFALNPGLLET-SEGCRQIIRQLQP-SIQTGSEEIKSLYNTVVTLYCVH-ERIKVASTKEALDKIEEE-QAKSK---KKAQQA--TADTRNSS------QVSQNYPIVQNLQ-GQMVHHPLSPRTLNAWVKVIEEKAFNPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPVAPGQLREPRGSDIAGTTSNLQEQIGWMTSN---PPIPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFYKTLRAEQASQDVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPSHKARVLAEAMS--QA--T---N--ANT-AIMMQRGNFKGPKKIIKCFNCGKEGHTAKNCRAPRKKGCWK-CGREGHQMKDCTERQANFLGKIWPSHNGRPGNFLQSRP----PA----EPTAPPA-----------EIFGLGEEIT-PPQKQEQ-KD--KEL---YPLTSLKSLFGNDPLSQ*- >Ref.F1.BR.93.93BR020_1.AF005494 MGARASVLSGGKLDAWEKIRLRPGGKKKYRLKHLVWASRELERFALDPGLLET-SEGCRKIIGQLQP-SLQTGSEELKSLYNTIAVLYYVH-QKVEVKDTKEALEKLEEE-QNKGR---QKTQQA--TAEKG----------VSQNYPIVQNLQ-GQMVHQSLSPRTLNAWVKVIEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPTQAGPIPPGQIREPRGSDIAGTTSTLQEQIQWMTGN---PPVPVGEMYKRWIILGLNKIVRMYSPVGILDIRQGPKEPFRDYVDRFFKTLRAEQATQEVKGWMTDTLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPSHKARVLAEAMS--QA--T---N--TA---IMMQKSNFKGQRRIVKCFNCGKEGHIAKNCRAPRKKGCWK-CGREGHQMKDCTERQANFLGKIWPSNKGRPGNFIQNRP----------EPSAPPA-----------ESFRFGEETT-PSPKQEQ-KD--EGL--YPPLASLKSLFGNDP!VTI! >Ref.D.CM.01.01CM_4412HAL.AY371157 --ARASILSGGKLDAWEKIRLRPGGSKKYRLKHLIWASNELERFALNPGLLET-SDGCKQILGQLQP-ALKTGTEELRSLFNAVAVLYCVH-ERIEVKDTKEALDKIEEE-QNKSK---KKAQQA--AADTGDNK------QVSQNYPIVQNLQ-GQMVHQALSPRTLNAWVKVIEEKAFNPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVQAGPVAPGQMREPRGSDIAGTTSTLQEQIGWMTSN---PPIPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFYKTLRAEQATQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVLAEAMS--QA--TAGMN--AA---IMMQRGNFKGPKRIVKCFNCGKEGHIAKNCRAPRKKGCWK-CGREGHQMKDCTERQANFLGKIWPSNKGRPGNFLQSRP----------EPTAPPA-----------ESFGFGEEIA-PSQKQEQ-KD--KDQE-LYPLTSLKSLFGNDPLSQ*- >Ref.F1.FR.96.96FR_MP411.AJ249238 MGARASVLSGGKLDAWERIRLRPGGKKKYRMKHLVWASRELERFAVDPGLLET-PEGCKQIIRQLQP-SLQTGSEELRSLFNTVAVLYCVH-QKIEIKDTKEALEKLEEE-QNKGQ---QKTQQA--AADKG----------VSQNYPIVQNLQ-GQMVHQPISPRTLNAWVKVIEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPAHAGPILPGQMREPRGSDIAGTTSTLQEQIQWMTSN---PPVPVGDIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFKTLRAEQASQEVKNWMTESLLVQNSNPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVLAEAMS--QA--T---N--AA---IMMQKSNYKGPRRFIKCFNCGKEGHIAKNCRAPRKKGCWK-CGKEGHQMKDCTERQANFLGKIWPSNKGRPGNFLQNRP----------EPTAPPA-----------ESFGFKEEIT-PSPKQEQ-KD--EGQGLYPPLASLKSLFGSDP!VTI! >Ref.A2.CY.94.94CY017_41.AF286237 MGARASILSGGKLDAWEKIRLRPGGKKKYRLKHLVWASRELEKFSINPGLLET-PEGCRQIIRQLQP-ALQTGTEELKSLYNTVVVLYWVH-QRVDVKDTKEALDKIEEE-QNK-----QKTQHA--AADTGNSS--------SQNYPIVQNAQ-GQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFTALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRVHPVHAGPIPPGQMREPRGSDIAGTTSTLQEQIGWMTSD---PPIPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFKTLRAEQATQEVKNWMTDTLLVQNANPDCRSILRALGPGASLEEMMTACQGVGGPSHKARVLAEAMSHVQS--T---N--TN---IMMQRGNFRGQKR-IKCFNCGKEGHLARNCRAPRKKGCWK-CGKEGHQMKDCTERQANFLGKIWPSNKGRPGNFPQSRT----------EPTAPPA-----------ENLRMGEEIT-SSLKQEL-ET--REP--YNPAISLKSLFGNDPLLQ*- >Ref.H.CF.90.056.AF005496 MGARASVLSGGKLDAWEKIRLRPGGKKKYRLKHLVWASRELERFALNPGLLET-PEGCLQIIEQIQP-AIKTGTEELKSLFNLVAVLYCVH-RKIDVKDTKEALDKIEEI-QNKSQ---QKTQQA--AADKEKDN------KVSQNYPIVQNAQ-GQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNAMLNTVGGHQAAMQMLKDTINEEAAEWDRVHPVHAGPIPPGQMREPRGSDIAGTTSTLQEQIAWMTGN---PAIPVGDIYKRWIILGLNKIVRMYSPVSILDIKQGPKEPFRDYVDRFFKTLRAEQATQDVKNWMTETLLVQNANPDCKTILRALGQGASIEEMMTACQGVGGPSHKARVLAEAMS--QV--T---N--TNT-AIMMQKGNFKGQRKFVKCFNCGKEGHIARNCRAPRKKGCWK-CGREGHQMKDCTERQANFLGKIWPSSKGRPGNFLQSRP----------EPTAPPA-----------ESFGFGEEMT-PSPKQEQLKD--KE----PPLASLRSLFGSDPLLQ*- >Ref.A2.CM.01.01CM_1445MV.GU201516 --ARASVLSGGKLDAWEKIRLRPGGRKKYRMKHLVWASRELEKYSINPGLLET-SEGCKQIIRQLHS-ALPVGTEELKSLYNTIAVLYYVH-QKIEVKDTKEALDKLEEE-QNKYK---QKTQQA--AAATGNSS--------SQNYPIVQNAQ-GQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRVHPVHAGPIPPGQMREPRGSDIAGTTSTLQEQIGWMTSN---PPIPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFKTLRAEQATQDVKNWMTDTLLVQNANPDCKTILRALGPAATLEEMMTACQGVGGPGHKARVLAEAMS--QIHST---N--QN---VMMQRGNFRGPKR-IKCFNCGKEGHLARNCRAPRKKGCWK-CGKEGHQMKDCTERQANFLGKIWPPNKGRPGNFPQSRT----------EPTAPPA-----------ENVGMGEEIA-SSSKQEL-RN--REQ--HTPTISLRSLFGNDPLSQ*- >Ref.A1.AU.03.PS1044_Day0.DQ676872 MGARASILSGGRLDAWEKIRLRPGGKKKYRLKHLVWASRELERFAL?P?LLES-AEGCQQIMEQLQP-A?KTG?EEIKSLFNTVATLYCVH-QRIDVKDTKEA?DKIEEI-KNKSK---QRTQQA--AADTGNSG------KVSQNYPIVQNAQ-GQMI?QNLSPRTLNAWVKVIEEKAFSPEVIPMFSALSEGATPQDLNVMLNIVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPIPPGQIREPRGSDIAGATSTPQEQLQWMTGN---PPIPVGDIYKRWIILGLNKIVRMYSPTSILDIRQGPKESFRDYVDRFFKALRAEQATQEVKSWMTETLLVQNANPDCKSILKALGSGATLEEMMTACQGVGGPSHKARVLAEAMS--QA--Q---Q--TS---IMMQRGNFRGGQKRIKCFNCGKEGHLARNCRAPRKKGCWK-CGKEGHQMKDCTERQANFLGKIWPSSKGRPGNFPQSRP----------EPTAPPA-----------ELFGMGEEIT-SPPKQEQ-KD--KEQ--VPPLVSLKSLFGNDPSSQ*- >Ref.J.SE.93.SE9280_7887.AF082394 MGARASILSGGKLDDWEKIRLRPGGKKKYRIKHLVWASRELDRFALNPGLLES-AKGCQQILVQLQP-ALQTGTQEIKSLYNTVATLYCVH-QRIEIKDTMEALEKIEEI-QNKNK---QQAQKA--ETDKKDNS------QVSQNYPIVQNLQ-GQPVHQALSPRTLNAWVKVIEEKAFSPEVIPMFSALSEGATPQDLNTMLNTIGGHQAAMQMLKDTINEEAAEWDRVHPVHAGPIAPGQVREPRGSDIAGTTSTLQEQIGWMTGN---PPIPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFKALRAEQATQDVKNWMTDTLLVQNANPDCKTILKALGSGATLEEMMTACQGVGGPGHKARVLAEAMS--QV--T---N--TN---IMMQRGNFRDHKRIVKCFNCGKQGHIAKNCRAPRKKGCWK-CGKEGHQMKDCTERQANFLGKIWPSSKGRPGNFLQSRP----------EPTAPPA-----------ESLGLGEEI--PSPKQEP-KD--KEL---YPLTSLKSLFGSDPLSQ*- >Ref.F2.CM.95.95CM_MP257.AJ249237 MGARASVLSGGKLDAWEKIRLRPGGKKKYRLKHIVWASRELKRFALNPGLLET-TEGCKKIIGQLQP-SLQTGSEELKSLFNTIVVLYYVH-QKIEVRDTKEALDKLQEE-QDKHQ---QKTQQA--TADKGVSK------GVSQNYPILQNLQ-GQMVHQSLSPRTLNAWVKVIEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPIPPGQMREPRGSDIAGTTSTLQEQIAWMTSN---PPVPVGEIYKRWIILGLNKIVRMYSPVSILDIKQGPKEPFRDYVDRFFKTLRAEQATQEVKGWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPSHKARILAEAMS--KA--T---G--AA---IMMQKSNFKGQRRIVKCFNCGKEGHIARNCRAPRKRGCWK-CGQEGHQMKDCTERQANFLGKMWPSNKGRPGNFLQNRP----------EPTAPPA-----------ESFGFGEEIA-PSPKQEQ-KD--KEQ--VPPLISLKSLFGS!PVVTI! >Ref.F2.CM.95.95CM_MP255.AJ249236 MGARASVLSGGKLDAWEKIRLKPGGKKRYRLKHLVWASRELERFALNPSLLET-TEGCKKIIGQLQS-SLQTGSEELKSLYNAVVVLYYVH-QRIDVRDTKEALDKLQEE-QDKSQ---QKEQQK--AADKE----------VSQNYPIVQNIQ-GQMVHQALSPRTLNAWVKVIEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPIPPGQMREPRGSDIAGTTSTLQEQITWMTGN---PPVPVGEIYKRWIILGLNKIVRMYSPVSILDIKQGPKEPFRDYVDRFFKTLRAEQATQEVKNWMTETLLVQNSNPDCKTILKALGPGATLEEMMTACQGVGGPGHKARILAEAMS--KA--T---S--TA---IMMQKSNFKGQKRIVKCFNCGKEGHIARNCRAPRKKGCWK-CGKEGHQMKDCTERQANFLGKIWPSNRGRPGNFLQNRP----------EPTAPPA-----------ENFGFGEGIT-PSPKQEQ-KG--EEQ--APPLVSLKSLFGSDP!SRN! >Ref.C.BR.92.BR025_d.U52953 MGARASILRGGKLDAWERIKLKPGGKKHYMMKHLVWASRELERFALDPGLLET-SEGCKQIMKQLQP-ALQTGTKELISLHNTVATLYCVH-EKIDVRDTKEALDKIKEE-QNKSQ---QKTQQA-EAADKG---------KVSQNYPIVQNLQ-GQMVHQPISARTLNAWVKVVEEKAFSPEVIPMFTALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPVAPGQMREPRGSDIAGTTSTLQEQITWMTNN---PPVPVGDIYKRWIILGLNKIVRMYSPVSILDIKQGPKEPFRDYVDRFFKTLRAEQATQDVKNWMTDTLLVQNANPDCKTILRALGPGASLEEMMTACQGVGGPGHKARVLAEAMS--KV--N---N--TN---IMMQRSNCKGPKRTIKCFNCGKEGHLARNCRAPRKKGCWK-CGKEGHQVKDCTERQANFLGKIWPSHRGRPGNLLQNRT----------EPTAPPE-----------ESFRFGEETTTPSRKQET-ID--KEL----PLTSLKSLFGSDPLST*- >Ref.G.KE.93.HH8793_12_1.AF061641 MGAR?S?LSGGKLDAWEKI?LTPGGKKKYRLKHLVWASREMERFALNPGLLET-AEGCQQIMSQLQP-AI?TGTEEIKSLFNTVATLYCVHP-KIEVKDTKEALEEVEKI-QKKSQ---QKIQQA--ARDEGNSS------QVSQNYPIVQNAQ-GQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRIHPPQAGPIPPGQIREPRGSDIAGTTSNLQEQIRWMTSN---PPIPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFKTLRAEQATQEVKGWMTDTLLVQNANPDCKTILRALGPGATLEEMMTACQGVGGPGHKARVLAEAMS--QA--T---G--AAA-AIMMQKSNFKGPKRNIKCFNCGKEGHLARNCRAPRKKGCWK-CGKEGHQMKDCTERQANF!GKIWPSNKGRPGNFLQNRP----------EPTAPPA-----------ESFGFGEEIA-PSPKPEP-KE--KEI---HPLASLKSLFGSDP!VTV! >Ref.A2.CD.97.97CDKTB48.AF286238 MGARASVLSGGKLEAWEKIRLRPGGKKKYRLKHLVWASRELEKFSINPSLLET-ETGCRRIFGQLQP-ALETGTEELRSLYNTIAVLYFVH-QKIEVKDTKEALDKIEEE-QNKCK---QKTQQA--AADTGSSSSQNYRGSSSQNYPIVQNAQ-GQMVHQAVSPRTLNAWVKVVEEKAFSPEVIPMFTALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVQAGPIPPGQMREPRGSDIAGATSNLQEQIGWMTSN---PPIPVGEIYKRWIILGLNKIVRMYSPVSILDIKQGPKEPFRDYVDRFFKTLRAEQATQEVKNWMTDTLLVQNANPDCKSILRALGPGATLEEMMTACQGVGGPGHKARVLAEAMS--QV--Q---N--TN---IMIQRGNFKGQKR-IKCFNCGKEGHLARNCRAPRKKGCWK-CGKEGHQMKDCTERQANFLGKIWPSNKGRPGNFPQSRT----------EPTAPPM-----------E-----EEIT-SSLKQEN-RE--PST----PAISLKSLFGNDLLSQ*- >Ref.G.BE.96.DRCBL.AF084936 MGARASVLSGGKLDAWEKIRLRPGGKKRYRMKHLVWASRELDRFALNPGLLET-AEGCQKIMAQLQP-ALQTGTEEIKSLFNTVATLYCVH-QKIEVRDTKEALEEVEKI-QKKSQ---QKENSS--S-------------QVSQNYPIVQNAQ-GQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFTALSEGATPQDLNTMLNTVGGHQAAMQMLKETINDEAAEWDRLHPQQAGPIAPGQIRDPTGSDIAGATSTLQEQIRWMTSN---PPVPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFKTLRAEQATQEVKSWMTDTLLIQNANPDCKIILKGLGQGATLEEMMTACQGVGGPSHKARVLAEAMS--QA--S---G--AAA-AIMMQKSNFKGPRRTIKCFNCGKEGHLARNCRAPRKKGCWK-CGKEGHQMKECTERQANFLGKIWPSNKGRPGNFLQNRP----------EPTAPPA-----------ENFGFGEEIA-PSPKQEQ-KE--KEL---YPLSSLKSLFGN!PIVKV! >Ref.K.CD.97.97ZR_EQTB11.AJ249235 MGARASVLSGGKLDKWEKIQLRPGGKKKYRLKHLVWASRELERFALNPNLLET-VEGCRQIIRQLQP-SLQTGSEELRSLFNTVATLYWVH-QSIQVRDTKEALDKLEEE-QNRTQ---QKTQQG--KADKG----------VSQNYPIVQNLQ-GQMVHQALSPRTLNAWVKVIEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRMHPVQAGPIPPGQIREPRGSDIAGTTSTLQEQITWMTSN---PPIPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFRVLRAEQATQEVKNWMTETLLVQNANPDCRTILKALGSGATLEEMMTACQGVGGPGHKARVLAEAMS--QV--T---N--SA---VMMQRGNFKGQRRIIKCFNCGKEGHLARNCRAPRKKGCWK-CGKEGHQMKDCSERQANFLGKFWPLNKERPGNFLQNRP----------EPTAPPA-----------ESFGFGEKIT-PSLRQEM-KD--QEQ--GPPLTSLKSLFGSDPLSQ*- >Ref.D.TZ.01.A280.AY253311 --ARASVLSGGQLDAWEKIRLRPGGKKKYQLKHIVWASRELERFALNPGLLET-SEGCKQI!---QP-AIQTGSEELKSLFNTVATLYCVH-RKIEVKDTKEALEKLEEE-QTKSK---KKAQQA--TADTGSSS------QVSQNYPIVQNLQ-GQMVHQAISPRTLNAWVKVIEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIAWMTNN---PPVPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFYKTLRAEQASQDVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPSHKARVLAEAMS--QA--T---N--VNA-AIMMQRGNFKGPRKIIKCFNCGKEGHIAKNCRAPRKKGCWK-CGKEGHQMKDCTERQANFLGKIWPSHKGRPGNFLQSRP----------EPTAPPA-----------EIFGFGEEIK-PSQKQEQ-KDKDKEL---YPSASLKSLFGNDPLSQ*- >Ref.F2.CM.02.02CM_0016BBY.AY371158 --ARASVLSGGKLDDWEKIRLRPGGKKKYRLKHIVWASKELERFALNPGLLET-TEGCKQIIGQLQ-SSLQTGSEEIKSLYNTVAVLYYVH-QKIQIRDTKEALDKLQEE-QDKYQ---QKTQPA--AADKG----------VSQNYPIVQNLQ-GQMVHQAISPRTLNAWVKVIEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVQAGPIPPGQIREPRGSDIAGTTSTLQEQIAWMTSN---PPVPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFKTLRAEQATQEVKGWMTDTLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARILAEAMS--QV--T---A--TS---VLMQKSNFKGQKRIVKCFNCGKEGHIAKNCRAPRKRGCWK-CGKEGHQMKDCTERQANFLGKIWPSNKGRPGNFIQSRP----------EPTAPPA-----------EGFGFGEEIT-PSPKQEQ-KD--KGL--YPPLTSLKSLFGNDP!VTI! >Ref.F1.BE.93.VI850.AF077336 MGARASILSGGKLDEWEKIQLRPGGKKRYKMKHLIWASRELERFALDPGLLET-SEGCQKIIRQLQP-SLQTGSEELKSLFNTVAVLYYVH-QRAGVTDTKEALDKLEEE-QNKSQ---QKTQQA--AADKG----------VSQNYPIVQNLQ-GQMVHQSLSPRTLNAWVKVIEEKAFSPEVIPMFSALSEGATPTDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPAPPGQMREPRGSDIAGTTSTLQEQIQWMTGN---PPVPVGDIYKRWIILGLNKIVRMYSPVSILDIKQGPKEPFRDYVDRFFKVLRAEQASQDVKGWMTDTLLVQNANPDCKTILKALGTGATLEEMMTACQGVGGPSHKARVLAEAMS--QA------N--SA---IMMQKSNFKGQRRVVKCFNCGKEGHIARNCRAPRKKGCWK-CGREGHQMKDCTERQANFLGKIWPSNKGRPGNFLQSRP----------EPTAPPA-----------ESFGFREEIT-PSPKQEQ-KD--GEL--YPPLASLKSLFGNDP!VTI! >Ref.B.NL.00.671_00T36.AY423387 MGARASVLSGGELDRWEKIRLRPGGKKRYKLKHIVWASRELERFAVNPGLLET-SEGCRQILGQLQP-ALQTGSEELKSLFNTVATLYCVH-ARIEVKDTKEALEKIEEE-QNKSKKRAQQAQQA--EADAGKNN------PVSQNYPIVQNLQ-GQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTNN---PPIPVGEIYKRWIILGLNKIVRMYSPTSILDIKQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNSNPDCKTILKALGPAATLEEMMTACQGVGGPGHKARVLAEAMS--QV--T---S--AP--AIMMQRGNHRNQRRTVKCFNCGKEGHIARNCRAP?KKGCWK-C?K?GHQMKDCT?RQA?FLGKIWPSHKGRPGNFLQSRPEPTAPSQSRPEPTAPPE-----------ESFRFGEETTTPSQRQEP-TD--KEL---YPLASLKSLFGSDP!VTI! >Ref.C.IN.95.95IN21068.AF067155 MGARASILRGGKLDKWEKIRLRPGGKKRYMLKHLVWASRELDRFAVNPGLLET-AEGCKQIIKQLQP-ALQTGTEELRSLFNTVATLYCVH-AGIEVRDTKEALDKIEEE-QNKIK---QKTQQA--KEDDG---------KVSQNYPIVQNLQ-GQMVHQAISPRTLNAWVKVIEEKAFSPEVIPMFTALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVPAGPIAPGQLREPRGSDIAGTTSTLQEQIAWMTNN---PPVPVGDIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFKTLRAEQATQDVKNWMTETLLVQNANPDCKTILRALGPGASLEEMMTACQGVGGPSHKARVLAEAMS--Q---T---N--SA---ILMQRSNFKGSKRIVKCFNCGKEGHLARNCRAPRKKGCWK-CGKEGHQMKDCTERQANFLGKIWPSHKGRPGNFLQSRP----------EPTAPPA-----------ESFRF-EETT-PAPKQEP-KD--RE-----PLTSLRSLFGSDPLSQ*- >Ref.B.US.98.1058_11.AY331295 ----ASVLSGGKLDTWEKIRLRPGGKKKYKLKHIVWASRELERFALNPGLLET-AEGCRQLLGQLQP-SLQTGSEELKSLFNTIATLYCVH-QRIEVRDTKEALDKIEEE-QNKSK---KKAQQAAAAADTGNSS------QVSQNYPIVQNLQ-GQMVHQAISPRTLNAWVKVIEEKAFSPEVIPMFAALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRIHPAQAGPIAPGQIRDPRGSDIAGTTSTLQEQITWMTNN---PPIPVGEIYKKWIIMGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPGHKARVLAEAMS--QV--T---N--SG--AIMMQKGNFRNQ--VVRCFNCGKVGHIAKNCRAPRKKGCWK-CGKEGHQMKDCDQRQANFLGKIWPSHKGRPGNFLQSRP----------EPTAPPA-----------ESFRFGEETTTPSQKQEP-QE--------YPLASLRSLFGNDPSSQ*- >Ref.J.CD.97.J_97DC_KTB147.EF614151 --------------AWEKIWLRRRGEKKYRRKHIVWASRELDRYALNPGLL!S!AEGGEQILVQIQP!SL!TGAEEIKSLFNTEATLYCVH!!RIDIRDTKEALDKIEE!L!NKSK---EKAKKE--AVKKYNS-------QVSHNYPILQNM!!GELVHQALSPRTLNAWVKVIEEKGFNPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPVAPGQMREPRGSDIAGTTSNLQEQIAWITGNGGNQPIPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFKTLRAEQATQEVKNWMTDTLLVQNANPDCKTILRALGAGATLEEMMTACQGVRVSSHRARVFGEAIS--QV--N---N--TN---IIMQRGNFRGQKRSVKCFNCGKEGHIAKNCRAPRKKGC!K!CGKEGHQIKNCTERQANFLGKVWPSSKGRPGNFLQSRP----------EPTAPPA-----------ESFGFGEKIT-PSQKQEP-R---KEL---YPSASLKSLFGSDPSSQ*- >Ref.J.CM.04.04CMU11421.GU237072 MGARASVLSGGKLDTWEKIRLRPGGKKRYRLKHLVWASRELDRFALNP?LLET-SKGCQQILVQLQP-SYQTGTEEIKSLYNTVATLYCVH-E?IEVKDTKE?LDKIEEL-QKKNK---QQAQKA--E?DK???S------QVSQNYPIVQNMQ-GQPV??ALSPRTLNAWVKV?E?KA?SPEVIPMFS?LSEGAT?QDLNTMLNT?GGH?AAMQMLKDTINEEAAEWDR?HPVHAGP?APGQAREPRGSDIAGTTSTLQEQIAWMTGN---PPIPVGEIYK?WIILGLNKI?RMYSPVSILDIRQGPK?PFR?YVDRFFKTLRAEQATQEVKNWMTDTLLIQNANPDCRT?LKALGPGATL?EMMTA?QGVGGPGHKARVL?EAMS--QM--T---N--TA--NIMMQ?G?FKG?KRMIKCFNC?KPGHL?R?CRAP??KGCWK-CGQEG?QMKDCTERQANFLG?IWPSN?GRPGNF?QS?P----------EPTAPPA-----------ESFGFGEE-T-??PKQEA-----KEL---YPLTSLKSLFG?DP?SQ*- >Ref.H.GB.00.00GBAC4001.FJ711703 MGARASVLSGGKLDAWEKIRLRPGGKKKYRLKHLVWASRELDRFALNPDLLET-ADGCLKI?GQIQP-ALQTGTEEIKSLFNLVAVLYCVH-QKIEVQDTSEALNKVKEI-QNKNQ---QTTQQA--TA?KEKDS------KISQNYPIVQNAQ-GQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALS?G?TPQD?NTMLNSVGGHQAAMQ?LKDTINEEAAEWDRTHPVHAGPIPPGQMREPRGSDIAGTT?NLQEQIAWMT?N---PP?PV??IYKRWII?GLNKIVRMYSPVSILDIKQGPKEPFR?YVDR?FKTLRAEQATQDVKNWMTDTLLVQNANPDCKTILKALGQGASIEEMMTACQGVGGPGHKARVLAEAMS--QM--T---N--MNT-AIMVQKGNFKGQRRTVKCFNCGKEGHIARNCRAPRKKGCWK-CGREGHQMKDCTERQANFLGKIWPSSKGRPGNFLQSRP----------EPTAPPA-----------ECFGFGEEMT-PPPKQEM-KE--KE----PPLTSLRSLFGSDPLSQ*- >Ref.G.NG.92.92NG083.U88826 VGARASVLSGGKLDSWEKIRLRPGGRKKYKLKHIVWASRELGRFALNRDLLET-AEGCVQIMKQLQP!SL!TGTEELRSLFNTVATLYCVH-QKIEVKDTKEAPEEVEKI-QKNSQ---QEIQQA--AKNEGNSN------PVSQNYPIVQNAQ-GQMIHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINDEAAEWDRIHPQQAGPIPPGQIREPSGSDIAGTTSTLQEQIRWMTSN---PPIPVGEIYKRWIILGLNKIVRMYSPVSILDIRQGPKEPFRDYVDRFFKTLRAEQATQEVKGWMTDTLLVQNANPDCKTILRALGPGATLEEMMTACQGVGGPSHKARVLAEAMS--QA--S---G--AAAAAIMMQKSNFKGPRRIIKCFNCGKEGHLARNCRAPRKKGCWK-CGKEGHQMKECTERQANFLGKIWPSNKGRPGNFLQNRT----------EPTAPPA-----------ESFGFGEEIA-PSPKQEP-KE--KEL---YPLTSLKSLFGSDP!VTV! >Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 MGARASVLSGGELDRWEKIRLRPGGKKKYKLKHIVWASRELERFAVNPGLLET-SEGCRQILGQLQP-SLQTGSEELRSLYNTVATLYCVH-QRIEIKDTKEALDKIEEE-QNKSK---KKAQQA--AADTGHSN------QVSQNYPIVQNIQ-GQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRVHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTNN---PPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPGHKARVLAEAMS--QV--T---N--SA--TIMMQRGNFRNQRKIVKCFNCGKEGHTARNCRAPRKKGCWK-CGKEGHQMKDCTERQANFLGKIWPSYKGRPGNFLQSRP----------EPTAPPE-----------ESFRSGVETTTPPQKQEP-ID--KEL---YPLTSLRSLFGNDPSSQ*- >Ref.B.TH.90.BK132.AY173951 MGARASVLSGGQLDRWEKIRLRPGGKKKYRLKHIVWASRELERFAVNPGLLET-SEGCRQILGQLQP-SLQTGSEELRSLYNTIAVLYCVH-QKIEVKDTKEALEKIEEE-QNKSK---KKAQQA--AANTENSS------QVSQNYPIVQNMQ-GQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHN---PPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPGHKARVLAEAMS--QV--T---N--SA--TIMMQKGNFRNQRKIVKCFNCGKEGHIARNCRAPRKKGCWR-CGKEGHQMKDCTERQANFLGKIWPSHKGRPGNFLQSRP----------EPTAPPA-----------ESFRFGEETTTPSQKQET-ID--KEL---YPLTALKSLFGNDPSSQ*- bppsuite-2.4.1/Examples/Data/HIV1_REF_2010_gag_macse_DNA.fasta000066400000000000000000002023411333524216000233360ustar00rootroot00000000000000>Ref.D.CD.83.ELI.K03454 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATAAATGGGAAAAAATTCGGTTACGGCCAGGAGGAAAGAAAAAATATAGACTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATATGCACTTAATCCTGGCCTTTTAGAAACA---TCAGAAGGCTGTAAACAAATAATAGGGCAGCTACAACCA---GCTATTCAGACAGGAACAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTACAT---AAAGGAATAGATGTAAAAGACACCAAGGAAGCTTTAGAAAAGATGGAGGAAGAG---CAAAACAAAAGTAAG---------AAAAAGGCACAGCAAGCA------GCAGCTGACACAGGAAACAACAGC------------------CAGGTCAGCCAAAATTATCCTATAGTGCAGAACCTACAG---GGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTGAACGCATGGGTAAAAGTAATAGAAGAAAAGGCTTTCAGCCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGCTAAAAGAGACCATCAATGAAGAAGCTGCAGAATGGGATAGGTTACATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGATATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGCATGGATGACAAGTAAC---------CCACCTATCCCAGTAGGAGAAATCTATAAAAGATGGATAATTGTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAGACAGGGACCAAAGGAACCTTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGATGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCAAACCCAGATTGCAAGACTATCTTAAAAGCATTGGGACCACAGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGGGGGCCCAGCCATAAAGCAAGAGTTCTGGCTGAGGCAATGAGC------CAAGCA------ACA---------AATTCAGTTACTACA---------GCAATGATGCAGAGAGGCAATTTTAAGGGCCCAAGAAAAATTATTAAGTGTTTCAATTGTGGCAAAGAAGGGCACATAGCAAAAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAGA---TGTGGAAAGGAAGGACACCAACTAAAAGATTGCACTGAGAGACAGGCTAATTTTTTAGGGAGAATTTGGCCTTCCCACAAGGGAAGGCCGGGGAACTTTCTCCAAAGCAGACCA------------------------------GAGCCAACAGCCCCACCAGCA---------------------------------GAGAGCTTCGGGTTTGGGGAAGAGATAACC---CCCTCTCAAAAACAGGAGCAG---AAAGAC------AAGGAACTG---------TATCCTTTAACTTCCCTCAAATCACTCTTTGGCAACGACCCCTTGTCGCAATAA--- >Ref.C.ET.86.ETH2220.U46016 ATGGGTGCGAGAGCGTCAATATTAAGAGGCGAAAAATTAGATGCCTGGGAAAAAATTAAGTTAAGGCCAGGGGGAAAGAAACACTATATGCTGAAACACCTAGTCTGGGCAAACAGGGAGCTGGAAAAATTTGCACTTAACCCTGACCTTTTAGATACA---TCAGCAGGCTGTAAACAAATAATTAAACAGCTACAACCA---GCTCTTCAGACAGGAACAGAGGAACTTAAATCATTATTTAATACAGTGGCAACTCTCTATTGTGTACAT---CAAAAGATAGAGATAAAAGACACCAAGGAAGCCTTAGACAAGATAGAGGAAGAA---CAAAACGAAAGTCAG---------CAAAAAACACAGCAGGCA---GGAGCAGCTGACAGAGGA---------------------------AAGGACAGTCAAAATTATCCTATAGTGCAGAATATGCAG---GGGCAAATGGTACATCAGCCCATATCAGCTAGAACTTTGAATGCATGGGTAAAAGTAGTAGAGGAAAAGGCTTTCAGCCCAGAGGTAATACCCATGTTTACAGCTTTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAATACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGACACCATCAATGAGGAGGCTGCAGAATGGGACAGGTTACATCCAGTGCATGCAGGGCCTGTTGCACCAGGCCAAATGAGAGACCCAAGGGGAAGTGACATAGCAGGAACAACTAGTACCCTTCAGGAACAAATAGCATGGATGACAGGGAAC---------CCACCTGTTCCAGTGGGAGACATCTATAAAAGATGGATAATCCTGGGGCTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAAACAAGGACCAAAGGAACCTTTTAGAGACTATGTAGACCGGTTCTTTAAAACCTTAAGAGCTGAACAAGCTACACAAGATGTAAAAAATTGGATGACAGACACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAAACCATTTTAAGAGCATTAGGGCCAGGGGCTTCATTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCTGCCCACAAAGCAAGAGTGTTGGCTGAGGCAATGAGC------CAAGTA------AAC---------AAT------ACAACC---------ATAATGATGCAGAAAAGCAATTTTAAGGGCCCTAAAAGAGCAATTAAATGTTTCAACTGTGGCAAGGAAGGGCACCTAGCCAGAAATTGCAGGGCCCCTAGGAAAAAAGGCTGTTGGAAA---TGTGGAAAGGAAGGACACCAAATGAAAGACTGTACCGAGAGACAGGCTAATTTTTTAGGGAGACTTTGGCCTTCCAACAAGGGAAGGCCAGGGAATTTCCTTCAGAGCAGACCA------------------------------GAGCCAACAGCCCCACCAGAGAGTCTCAGACCAGAGCCAACAGCCCCACCACCAGAGAGCTTCAGGTTC---GAGGAAGCAACA---CCTTCTCCGAAGCAGGAGCTG---AAAGAC------AGGGAA---------------GCCTTAACTTCCCTCAAATCACTCTTTGGCAACGACCACTTGTTACAATAA--- >Ref.C.ZA.04.04ZASK146.AY772699 ATGGGTGCGAGAGCGTCAGTATTAAGAGGCGAAAAATTAGATACATGGGAAAAAATTAGGTTAAGGCCAGGGGGAAAGAAACACTATATGCTAAAACACATAGTATGGGCAAGCAGGGAGCTGGAAAGATTTGCACTCAACCCTGGCCTTTTAGAAACA---TCAGAAGGCTGTAAACAAATATTGGCACAAATACAACCA---GCTATTCAGACAGGAACAGAGGAACTTAAATCATTATTCAACACAATAGCAGTTCTCTATTGTGTACAT---AAAAAGATAGATGTAAGAGACACCAAGGAAGCCTTAGACAAGATAGAGGAAGAG---CAAAACAAAAGTCAG---------CAAAAAACACAGCAGGCA---AAAGCGGCTGACGAA------------------------------AAGGTCAGTCAAAATTTTCCTATAGTACAGAATCTTCAA---GGGCAAATGGTACATCAACCCCTATCACCTAGAACCTTGAATGCATGGGTAAAAGTAATAGAGGAGAAGGGTTTTAACCCAGAGGTAATACCCATGTTTACAGCATTATCAGAGGGAGCCACCCCACAAGATTTGAACACCATGCTAAATACGGTGGGGGGACATCAAGCAGCCATGCAGATGTTAAAAGATACCATCAATGAAGAGGCTGCAGAATGGGATAGATTACATCCAGTACATGCAGGGCCTGTCGCACCAGGCCAAATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTAACCTTCAGGAACAAGTAGCATGGATGACAAGTAAC---------CCACCTATTCCAGTGGGAGACATCTATAAAAGATGGATAATTCTGGGATTAAATAAAATAGTGAGGATGTATAGCCCGGTCAGCATTTTGGACATAAAACAAGGGCCAAAGGAACCCTTTAGAGACTATGTAGATCGGTTCTTTAAAACTTTAAGAGCTGAACAAGCTACACAAGAGGTAAAAAATTGGATGACAGACACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACCATTTTAAGAGCATTAGGACCAGGGGCTACATTAGAAGAAATGATGGCAGCATGTCAAGGGGTGGGAGGACCTGGCCACAAGGCAAGAGTGTTGGCTGAGGCAATGAGC------CAAATA------AAC---------AAT------GGAAAC---------ATAATGATGCAGAGAAGTAATTTTAAAGGCCCTAAAAGAATTGTTAAATGTTTTAACTGTGGCAAGGGGAGGCACATAGCCAAAAATTGCAGGGCCCCTAGGAAAAAAGGCTGTTGGAAA---TGTGGAAAGGAAGGACACCAAATGAAAGACTGTACTGAAAGGCAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCCAGAAGGGGAGGCCAGGGAATTTTCTCCAGAACAGACTA------------------------------GAGCCAACAGCCCCACCAGCA---------------------------------GAGAGCTTCAGGTTC---GAGGAGACGACC---CCTGCTCCGAAACAGGAGCTG---AAAGAC------AGGGAA---------------CCTTTAACTTCCCTCAGATCACTCTTTGGCAGCGACCCCTTGTCTCAATAA--- >Ref.A1.UG.92.92UG037.AB253429 ATGGGTGCGAGAGCGTCAGTATTAAGTGGGGGAAAATTAGATGCATGGGAGAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAGATTAAAACATCTAGTATGGGCAAGCAGGGAGCTGGAAAGATTTGCACTTAACCCTAGCCTTTTAGAAACA---ACAGAAGGATGTCAACAAATAATGGAACAATTACAATCA---GCTCTCAGAACAGGAACAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGCGTACAT---CAACGGATAGAGGTAAAAGACACCAAGGAAGCTCTAGATAAAATAGAGGAGATA---CAAAAGAAAAGCAAG---------CAAAAGACACAGCAGGCA------GCAGCTGACACAGGAAGTAGCAGC------------------AAGGTCAGCCAAAATTACCCTATAGTGCAAAATGCACAA---GGGCAAATGATCCACCAGTCCTTGTCACCTAGGACTTTGAATGCATGGGTGAAAGTAATAGAAGAAAAGGCTTTCAGCCCAGAAGTAATACCCATGTTCTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTGAATATGATGCTGAACATAGTGGGGGGACACCAGGCAGCTATGCAAATGTTAAAAGATACCATCAATGAGGAAGCTGCAGAATGGGACAGGCTACATCCAGTACATGCAGGGCCTGTTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGATATAGCAGGAACTACTAGTACCCCTCAAGAACAAATAGCATGGATGACAGGCAAC---------CCACCTATCCCAGTGGGAGACATCTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTTAGCATTTTAGATATAAAACAAGGGCCAAAAGAACCCTTCAGAGACTATGTAGATAGGTTTTTTAAAACTCTCAGAGCTGAGCAAGCTACACAGGAGGTAAAAGGTTGGATGACAGAAACATTACTGATCCAAAATGCAAATCCAGATTGTAAATCCATCCTAAGAGCATTAGGAGCAGGGGCTACATTAGAAGAAATGATGACAGCATGCCAGGGAGTGGGAGGACCCGGCCATAAAGCAAGAGTTTTGGCTGAGGCAATGAGT------CAAGTA------CAA---------CAT------ACAAAC---------ATAATGATGCAGAGAGGCAATTTTAAGGGCCAGAAAAGG---ATTAAGTGTTTCAACTGTGGCAAAGAAGGACATCTAGCCAAAAATTGCAGGGCTCCTAGAAAAAAGGGCTGTTGGAAA---TGTGGAAGGGAAGGGCACCAAATGAAGGACTGCACTGAGAGACAGGCTAATTTTTTAGGGAAAATCTGGCCTTCCAGCAAAGGGAGGCCAGGAAATTTTCCTCAGAGCAGACCA------------------------------GAACCAACAGCCCCACCAGCAGCA------------------------------GAGATCTTTGGGATGAGGGAAGAGATAGTC---TCCCCTCCGAAGCAGGAGCAG---AACGAC------AGGGACCAG------AACCCACCTTCAGTTTCCCTCAAATCACTCTTTGGCAACGACCTCTTGTCACAGTAA--- >Ref.A1.RW.92.92RW008.AB253421 ATGGGTGCGAGAGCGTCAGTATTAAGTGGGGGAAAATTAGATGCATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAGAATGAAACATCTAGTATGGGCAAGCAGGGAGCTGGAAAGATTTGCACTTAACCCTGGCCTTTTAGAAACA---ACAGAAGGATGTCAAAAAATAATAGAACAGTTACAACCA---TCTGTCAAGACAGGAACAGAAGAACTTAAATCATTATTTAATACAGTAGCAACCCTCTATTGCGTACAT---CAACGGATAGATGTAAAAGACACCAAGGAAGCCCTAGATAAAATAGAGGAAATG---CAAAATAAGAGCAAG---------CAAAAGACACAACAGGCA------GCAGCTGACATAGGAAATAGCAGC------------------AAGGTCAGCCAAAATTACCCTATAGTGCAAAATGCACAA---GGGCAAATGATATATCAGTCCATGTCACCTAGGACTTTGAATGCATGGGTGAAAGTAATAGAAGAAAAGGGTTTCAACCCAGAAGTAATACCCATGTTCTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAATATGATGCTAAACATAGTGGGGGGACATCAGGCAGCTATGCAAATGTTAAAAGATACCATCAATGAGGAAGCTGCAGACTGGGACAGGTTACATCCAGTACAGGCAGGGCCTATTCCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCCTCAAGAACAAATAGGATGGATGACAAGCAAC---------CCACCTATCCCAGTGGGAGACATCTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTTAGCATTTTGGATGTAAAACAAGGGCCAAAAGAACCCTTTAGAGATTATGTAGATAGGTTCTTTAAAATTCTCAGAGCTGAACAAGCTACACAGGATGTAAAACATTGGATGACAGAAACATTGCTGATCCAAAATGCAAATCCAGATTGTAAGTCCATTTTAAGAGCATTAGGAACAGGGGCTACATTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCCAGCCATAAAGCAAGGGTTTTAGCTGAGGCAATGAGT------CAAGTA------CAA---------CAT------CCAAAC---------ATAATGATGCAGAGAGGCAATTTTAGGGGCCAGAAAAGG---ATTAAGTGCTTCAACTGTGGCAAAGAAGGACACCTAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAA---TGTGGAAAGGAGGGACACCAAATGAAAGACTGCACTGAAAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAGCAAGGGGAGGCCAGGAAATTTTCCTCAGAGCAGACCG------------------------------GAGCCATCAGCCCCACCAGCA---------------------------------GAGATCTTTGGGATAGGGGAAGAGATAGCC---TCCCCTCCGAAGCAGGAGCAG---AAAGAC------AGGGAACCG------GCCCAACCTTTAGTTTCCCTCAAATCACTCTTTGGCAACGACCCCTTGTCACAGTAA--- >Ref.H.BE.93.VI997.AF190128 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGACGATTAGATACTTTGGAGAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAGGCTAAAACATATAGTATGGGCAAGCAGAGAGCTGGAAAGATTTGCACTTAACCCCGGCCTTTTAGAATCA---GCAGAAGGCTGTCTACAAATAATAGAACAACTACGGCCA---TCTATTAAGACAGGAACAGAAGAACTTCWATCATTATTTAATACCGTAGCGACCCTCTATTGCGTACTT---CAAAGAATAGAGGTAAAAGACACCAAGGAAGCTTTAGGGAAGATAGAGGAAATA---CAAAACAAAAGGCAG---------CAAAAAACACAGCAAGCA------ACAGCTAATAAGGAAAGAGACAAC------------------AAGGTCAGTCAAAATTATCCTATAGTACAGAATGCTCAA---GGGCAGATGGTACACCAGCCCATATCACVTAGGACCTTAAATGCATGGGTAAAAGTAGTAGAGGAGAAGGCTTTTAGCCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGACTTAAATGCTATGCTAAATACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACAATCAATGAGGAAGCTGCAGAATGGGATAGGCTACATCCAGTGCATGCAGGGCCTATTCCACCAGGCCAGATGAGAGAACCAAGGGGAAGCGATATAGCTGGAACTACTAGTACCCTTCAGGAACAAATAGCATGGATGACAGGCAAT---------CCAAGTATCCCAGTGGGAGACATCTATAAAAGATGGATAATCCTGGGATTAAATAAGATAGTAAGAATGTATAGTCCTGTTAGTATTCTGGACATAAAACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTCTTTAAAACTTTAAGAGCTGAGCAAGCCACACAGGAGGTGAAGAATTGGATGACAGACACCTTGTTGGTCCAGAATGCAAATCCAGATTGCAAGACTATTTTAAGAGCATTAGGACAAGGGGCTTCAATAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCTAGTCATAAAGCAAGAGTTTTGGCTGAGGCAATGAGC------CAAGTA------ACA---------AAT------GCAAATGCA---GCCATAATGATGCAGAAAAGCAACTTTAAGGGCCCAAGAAAAATTGTTAAATGTTTCAATTGTGGCAAAGAGGGACACATAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAA---TGTGGAAGGGAAGGACATCAGATGAAGGACTGCACAGAGAGACAGGCTAATTTTTTAGGGAAAATCTGGCCTTCCAGCAAAGGGAGGCCAGGAAATTTTCTCCAGAGCAGGCCA------------------------------GAGCCAACAGCCCCACCAGCA---------------------------------GAGAGCTTCGGGTTCGGGGAGGAGATGACC---TCCTCCCCGAAGCAGGAGCTG---AAGGAC------AAGGAA------------CCTCCCTTTGCTTCCCTCAAATCACTCTTTGGCAACGACCCCTTGTCACAGTAA--- >Ref.H.BE.93.VI991.AF190127 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCTTGGGAGAAAATTCGGTTAAGGCCAGGGGGAAGGAAAAAATATAGGCTAAAACATCTGGTATGGGCAAGCAGGGAGCTGGAAAGATTTGCACTTAACCCCGACCTTTTAGAAACA---GCAGATGGCTGCCAACAAATACTAGGACAGCTACAGCCA---GCTCTTAAGACAGGAACAGAAGACCTTCAATCATTATATAATACAATAGCAGTCCTCTATTGCGTACAT---CAAAGAATAGATGTGAAAGACACCAAGGAAGCTTTAGGGAAGATAGAGGAAATA---CAGAATAAGAACAAG---------CAAAGAACACAGCAGGCCCCAGCAGCAGCTGATAAAGAAAAGGACAGC------------------AAGATCAGTCAAAATTATCCTATAGTACAGAATGCCCAG---GGGCAAATGGTACACCAGGCAATATCACCTAGGACCTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTTAGCCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGACTTAAATGCCATGCTAAATACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACAATCAATGAGGAAGCTGCAGAATGGGATAGGCTACATCCAGTACATGCAGGGCCTATTCCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGATATAGCAGGAACTACTAGTACCCTTCAGGAACAAGTAGCATGGATGACAGGCAAT---------CCCCCAATTCCAGTGGGAGACATCTATAAGAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAAACAAGGACCAAAAGAACCCTTCAGAGACTATGTAGACAGGTTCTTTAGAGTTTTAAGAGCTGAGCAAGCTACACAGGATGTAAAAAACTGGATGACAGACACCTTGTTGGTCCAAAATGCGAATCCAGATTGCAGGACTATTTTAAAAGCATTAGGACGAGGGGCTTCAATAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCAAGCCATAAAGCAAGAGTTTTGGCTGAGGCAATGAGC------CAAGTA------ACA---------AAT------GCAAGTGCA---GCCATAATGATGCAGAAAGGCAACTTTAAGGGCCCAAGAAGAACTGTTAAATGTTCCAACTGTGGCAAAGAAGGACACATAGCCAGAAATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAA---TGTGGACAGGAAGGACACCAGATGAAAGACTGCACAGGAAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAGCAAGGGAAGGCCAGGGAATTTCCCCCAGAAGAGGCTA------------------------------GAGCCAACAGCCCCACCAGCA---------------------------------GAGAGCTTCGGGTTCGGAGAGGAGATCACC---CCCTCTCCGAGGCAGGAGCTG---AAAGAA------CAGGAA------------CCTCCTTTAACTTCCCTCAGATCACTCTTTGGCAAC!GACCAATAGTCACAGTA!!A >Ref.G.PT.x.PT2695.AY612637 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCATGGGAAAAAATTCGGTTGAGGCCAGGGGGAAAGAAAAAATATAGAATGAAACATTTAGTATGGGCAAGCAGGGAGCTGGAAAAATTTGCACTCAACCCTGACCTTTTAGAAACA---GCAGAAGGTTGTCAACAAATAATGAGACAGTTACAACCA---GCTCTCCAGACAGGAACAGAGGAGCTTAGATCATTATTTAATACAGTAGCAACACTCTATTGTGTACAT---CAAAGGATAGAGGTAAAAGACACCAAAGAAGCTCTAGAGGAAGTGGAAAAGACA---CAGAAGAAAAGT------------CAGAAACAACAGCAGGCA------GCAATGGACGAAGGAAACAGCAGC------------------CAAGTCAGCCAAAATTATCCTATAGTGCAGAATGCACAA---GGGCAAATGGTACATCAGGCCATATCACCCAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAAAAGGCCTTCAGTCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCGCAAGATTTAAATACCATGCTAAACACAGTAGGGGGGCATCAAGCAGCTATGCAAATGCTAAAGGATACTATTAATGAGGAAGCTGCAGAGTGGGACAGGATACATCCACAACAGGCAGGGCCTATCCCACCAGGCCAGATAAGAGAACCAAGGGGAAGTGATATAGCAGGAACTACTAGTACCCTGCAGGAACAAATAAGATGGATGACCAGCAAT---------CCACCTATCCCAGTGGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGATATAAGACAAGGGCCAAAAGAACCTTTTAGAGATTATGTAGATAGGTTCTTTAAAACTTTAAGAGCTGAACAAGCTACACAGGAAGTAAAAGGCTGGATGACAGACACCTTGCTGGTCCAAAATGCGAACCCAGATTGTAAGACCATCTTAAGAGCATTAGGACCAGGAGCTTCACTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCCAGTCACAAAGCAAGAGTTTTAGCTGAGGCAATGAGC------CAGGCA------TCA---------GGG------GCAACA---------ATAATGATGCAAAAAAGCAACTTTAAGGGTCCAAAAAGAATGATTAAGTGTTTCAACTGTGGCAAGGAAGGACACCTAGCTAGAAATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAA---TGTGGAAAGGAGGGACACCAAATGAAAGACTGCACAGAGAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAACAAGGGGAGGCCAGGGAATTTTCTCCAGAACAGGCCC------------------------------GAGCCAACAGCCCCACCCGCA---------------------------------GAGAGCTTCGGGTTCGGAGAGGAGATAGCC---CCCTCCCCGAAGCAAGAGCCG---AAGGAC------AAGGAGTTA---------TACCCCTTAACCTCCCTCAAATCACTCTTTGGCAGCGACCCC!TAGTCACAGTA!!A >Ref.K.CM.96.96CM_MP535.AJ249239 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCATGGGAAAAGATTCGGTTACGGCCAGGGGGAAAGAAAAAATATAAACTGAAACATCTAGTATGGGCAAGCAGGGAGCTAGAACGATTTGCACTCAACCCTGGCCTTTTAGAGACA---ACAGAAGGCTGTCGGCAAATAATAACACAAATACAGCCA---TCCATTCAAACAGGATCAGAAGAGATTAAATCACTATATAATACAATAGCAGTCCTCTATTTTGTACAT---CAAAAGATAGAGGTAAAAGACACCAAGGAAGCCTTAGACAAACTAGAGGAAGAA---CAAAACAAAAGTCAG---------CGAAAGACACAACAAGAA------GCAGCTGACAAAGGG------------------------------GTCAGTCAAAATTACCCTATAGTACAGAATCTGCAG---GGGCAAATGGTACACCAGGCCCTATCACCTAGAACTTTAAATGCATGGGTGAAGGTAATAGAGGAGAAGGCTTTCAGCCCAGAAGTAATACCCATGTTTACAGCATTATCAGAAGGAGCCACTCCACAAGATCTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACTATCAATGATGAAGCTGCAGAATGGGACAGGTTACACCCAGTGCATGCAGGGCCTATCCCACCAGGCCAAATGAGAGAACCGAGGGGGAGTGACATAGCAGGAACTACCAGCACCCTTCAGGAACAAATAGCATGGATGACAAGCAAC---------CCACCTGTCCCAGTGGGGGAAATCTATAAAAGATGGATAATCCTGGGTTTAAACAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAGACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGATAGGTTCTTTAAAACCCTAAGAGCTGAACAAGCCACACAGGAAGTAAAGAATTGGATGACAGACACCCTGTTGGTCCAAAACGCAAACCCAGATTGTAAGACCATTTTAAAAGCGTTGGGACCAGGGGCTTCATTAGAAGAGATGATGACAGCATGTCAGGGAGTGGGAGGGCCTAGCCATAAAGCAAGAATTTTGGCTGAGGCAATGAGC------CAGGTA------ACA---------AAT------CCAGTT---------GTAATGATGCAGAAAGGCAACTTTAAGGGCCATAGAAAAATTGTTAAGTGCTTCAACTGTGGCAAAGAAGGGCACATAGCCAGAAATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAA---TGTGGGAAGGAAGGACATCAGATGAAAGACTGCACTGAGAGACAGGCTAATTTTTTAGGGAAAATCTGGCCTTCCCACAAGGGGAGGCCAGGGAATTTTCTTCAGAGCAGACCA------------------------------GAGCCAACAGCCCCACCAGCA---------------------------------GAGAGCTTCGGGTTCGGGGAGGAGATAACC---CCCTCTCCGAGGCAGGAGACC---AAAGAC------AAGGAACAG------AGCCCTCCTTTAACTTCCCTCAAATCACTCTTTGGCAACGACCCATTGTCACAATAA--- >Ref.F2.CM.97.CM53657.AF377956 ---------AGAGCGTCACTATTAAGCGGGGGAAAATTAGATGATTTGGAAAAAATTCGGTTAAGGCCAGGGGGGAAGAAAAAATATAGGCTGAAACATATAGTATGGGCAAGCAGGGAGCTAGAAAGATTTGCACTTAATCCTGGCCTTTTAGAGACAAAG---GAAGGCTGTAAACAAATAATAGGACAACTACAACCA---TCCCTTCAGACAGGATCAGAAGAGCTTAAATCATTATTCAACACAATAGTAGTCCTCTATTATGTACAT---CAAAGGATAAAAATAGGAGACACCAAGGAAGCTTTAGATAAGCTACAGGAAGAA---CAAGACAAAAGTCAG---------CAAAAAACACAACCAGCA------GCGGCTGACAAAGGG------------------------------GTCAGTCAAAATTACCCTATAGTACAGAATCTTCAG---GGACAAATGGTACACCAGTCTCTATCACCTAGAACTTTAAATGCATGGGTAAAAGTAATAGAAGAGAAGGCTTTCAGCCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACCATCAATGAGGAAGCTGCAGAATGGGACAGATTACATCCAGTGCAGGCAGGACCCATCCCACCAGGTCAGATAAGAGAACCTAGGGGAAGTGATATAGCAGGAACTACTAGCAACCTACAGGAACAAATAGCATGGATGACAAGCAAC---------CCACCTGTCCCAGTAGGAGAAATCTATAAAAGATGGATAATCCTAGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAAACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTCTTTAAAACTCTAAGAGCTGAGCAAGCTTCACAGGAAGTAAAAGGCTGGATGACAGACACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGATCATTTTAAAAGGATTAGGAACAGGGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGGGTGGGGGGACCTGGCCATAAGGCAAGAATTTTGGCTGAGGCAATGAGC------CAAGTA------ACA---------TCT------ACATCC---------ATATTGATGCAGAAAAGCAACTTTAAGGGCCAAAGAAGAAATGTTAAGTGTTTCAACTGTGGCAAAGAAGGACATATAGCTAAAAATTGCAGGGCCCCTAGAAAAAGGGGCTGTTGGAAA---TGTGGAAAGGAAGGACACCAAATGAAAGACTGCACTGAGAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAACAAGGGGAGGCCTGGAAATTTTCTTCAGAACAGACCA------------------------------GAGCCAACAGCCCCGCCAGCA---------------------------------GAAAGCTTCGGGTTCGGAGAAGAGATAACT---CCCTCCCCGAAGCAGGAGCAG---AAAGAC------AAGGAAATG------TACCCTCCCTTGACTTCCCTCAAATCACTCTTTGGCAACGACCCT!TAGTCACAATA!!A >Ref.F1.FI.93.FIN9363.AF075703 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAACTAGATGCATGGGAAAAAATTCGGTTAAGGCCGGGGGGAAAGAAACAATATAGAATAAAACATCTAGTATGGGCAAGCAGGGAGCTAGAACGATTTGCAATAGATCCTGGCCTTCTAGAAACA---TCAGAAGGCTGTCAAAAAATAATAGCACAGATACAGCCA---TCCATTCAGACAGGATCAGAAGAGCTTAGATCATTATATAACACAATAGCAGTCCTCTATTTTGTACAT---CAAAAGATAGAGGTAAAGGACACCAAGGAAGCTTTAGATAAGCTAGAGGAAGAA---CAAAACAAAAGTCAG---------CAAAAGACACAGCAAGCGGCAGCTGCAGCTGACAAAGGG------------------------------GTCAGTCAAAATTACCCTATAGTACAGAATCTTCAG---GGACAAATGGTACATCAGGCTATATCACCTAGAACTTTAAATGCATGGGTAAAGGTGATAGAAGAGAAGGCTTTTAGCCCAGAAGTTATACCCATGTTTTCAGCATTATCAGAAGGGGCCACTCCACAAGATTTAAACACCATGCTAAATACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGACACCATTAATGAGGAAGCTGCAGAATGGGACAGATTACATCCAGTGCATGCAGGACCTATTCCACCAGGCCAGATGAGGGAACCTAGGGGAAGCGATATAGCTGGAACTACTAGTACCCTTCAGGAACAAATACAATGGATGACAAGTAAC---------CCACCTGTCCCAGTGGGAGACATCTATAAAAGATGGATCATCCTAGGATTAAATAAAATAGTAAGGATGTATAGCCCTGTCAGCATTTTGGACATAAGACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTCTTTAAAGCTCTAAGAGCTGAGCAAGCTACACAGGAAGTAAAGGGTTGGATGACAGACACCTTGTTGGTCCAAAATGCGAATCCAGATTGTAAGATCATTTTAAAAGGATTGGGAATAGGGGCTACACTAGAAGAAATGATGACAGCATGTCGGGGAGTGGGAGGACCTGGCCATAAGGCAAGAATTTTGGCTGAGGCAATGAGC------CAAGCA------------------AAT------ACAACC---------ATAATGATGCAGAAAAGTAATTTTAGGGGCCAAAGAAGAATTGTTAAATGTTTTAATTGTGGCAAAGAAGGACACATAGCCAGAAATTGCAGGGCCCCCAGGAAAAAGGGCTGTTGGAAA---TGTGGACAAGAAGGGCACCAAATGAAAGACTGCACTGAAAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAACAAGGGGAGGCCCGGAAATTTCCTTCAGAGTAGACCA------------------------------GAGCCAACAGCCCCGCCAGCA---------------------------------GAGAGCCTCGGGATCAGAGAAGAGGTAACT---CCCTCTCCGAGGCAGGAGCAG---AAAGAA------GAGGGACAG------TACCCTCCCTTAGCTTCCCTCAAATCACTCTTTGGCAACGACCCC!TAGTCACAATA!!A >Ref.D.UG.94.94UG114.U88824 ATGGGTGCGAGAGCGTCAGTATTAAGCGGAGGAAAATTAGATGAATGGGAAAAAATTCGGTTACGGCCAGGGGGAAAGAAAAAATATAGACTAAAACATCTAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCACTTAATCCTGGCCTTTTAGAAACA---TCAGAAGGCTGTAGACAAATAATAAGACAGCTACAACCA---TCTATTCAGACAGGATCAGAGGAAATTAAATCATTATATAATACAGTGGTAACCCTCTATTGTGTACAT---GAGAGGATAAAGGTAGCAAGCACCAAGGAAGCTTTAGACAAGATAGAGGAAGAA---CAAGCCAAAAGTAAG---------AAAAAAGCACAGCAAGCA------ACAGCTGACACAAGAAACAGCAGC------------------CAGGTCAGCCAAAATTATCCTATAGTGCAAAACCTACAG---GGGCAAATGGTACACCATCCCCTATCACCTAGAACTTTGAACGCATGGGTAAAAGTAATAGAGGAGAAGGCTTTCAACCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAATACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAGGATACCATCAATGAGGAAGCTGCAGAATGGGATAGGCTACATCCAGTGCATGCAGGGCCTGTTGCACCAGGCCAATTGAGAGAACCAAGGGGAAGTGATATAGCAGGAACTACTAGTAACCTTCAGGAACAAATAGGATGGATGACAAGCAAT---------CCACCTATCCCAGTAGGAGAAATCTATAAAAGATGGATAATCCTAGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGATCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGATGTAAAAAATTGGATGACTGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAAACTATCTTAAAAGCATTGGGACCAGCGGCTACATTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGGGGACCCAGTCATAAAGCAAGAGTTTTGGCTGAGGCAATGAGC------CAAGCA------ACA---------AAT------GCAAATACT---GCTATAATGATGCAGAGAGGCAATTTTAAGGGCCCAAAGAAAATCATTAAGTGTTTCAACTGTGGCAAAGAAGGGCACACGGCAAAAAATTGCAGGGCTCCTAGAAAAAAGGGCTGTTGGAAA---TGTGGAAGGGAAGGACACCAAATGAAAGATTGCACTGAAAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCCACAATGGAAGGCCAGGGAATTTCCTTCAGAGCAGACCC------------CCAGCA------------GAGCCAACAGCCCCACCAGCA---------------------------------GAGATCTTCGGATTAGGGGAGGAGATAACA---CCTCCTCAGAAACAGGAGCAG---AAAGAC------AAGGAACTG---------TATCCTTTAACCTCCCTCAAATCACTCTTTGGCAACGACCCGTTGTCACAGTAA--- >Ref.F1.BR.93.93BR020_1.AF005494 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCTTGGGAAAAAATTCGGTTAAGGCCGGGGGGAAAGAAAAAATATAGACTAAAACATCTAGTATGGGCAAGCAGGGAGCTAGAACGATTTGCACTTGATCCAGGCCTTCTAGAAACA---TCAGAAGGCTGTCGAAAAATAATAGGACAGTTACAACCA---TCCCTTCAGACAGGATCAGAAGAGCTCAAATCATTATATAATACAATAGCAGTCCTCTATTATGTACAT---CAAAAGGTAGAGGTAAAAGACACCAAGGAGGCTTTAGAGAAGCTAGAGGAAGAA---CAAAACAAAGGTCGG---------CAAAAGACACAGCAAGCG------ACTGCTGAAAAAGGG------------------------------GTCAGTCAAAATTACCCTATAGTACAGAATCTTCAG---GGACAAATGGTACACCAGTCTTTATCACCTAGAACTTTAAATGCATGGGTAAAGGTGATAGAAGAGAAGGCTTTTAGTCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGGGCCACTCCACAAGATTTAAACACCATGTTAAATACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGACACCATCAATGAGGAGGCTGCAGAATGGGACAGATTACATCCAACACAGGCAGGACCCATCCCCCCAGGTCAGATAAGGGAACCTAGGGGAAGTGATATAGCTGGAACTACTAGTACCCTTCAGGAACAAATACAATGGATGACAGGCAAC---------CCACCTGTCCCAGTGGGAGAAATGTATAAAAGATGGATCATCCTAGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTCGGCATTTTGGACATAAGACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTCTTTAAAACCCTAAGAGCTGAGCAAGCTACACAGGAAGTAAAGGGTTGGATGACAGACACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACCATTTTAAAAGCATTGGGACCAGGGGCTACACTAGAGGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCTAGCCATAAGGCAAGAGTTTTGGCTGAGGCAATGAGC------CAAGCA------ACA---------AAT------ACAGCT---------ATAATGATGCAGAAAAGTAACTTTAAGGGCCAAAGAAGAATTGTTAAATGCTTTAATTGTGGCAAAGAAGGACACATAGCCAAAAATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAG---TGTGGAAGAGAGGGACACCAAATGAAGGACTGCACTGAGAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAACAAGGGGAGGCCCGGAAACTTCATCCAGAACAGGCCA------------------------------GAGCCGTCAGCCCCGCCAGCA---------------------------------GAGAGCTTCAGGTTCGGGGAGGAGACAACC---CCATCTCCGAAGCAGGAGCAG---AAAGAC------GAGGGACTG------TACCCTCCCTTAGCTTCCCTCAAATCACTCTTTGGCAACGACCCC!TAGTCACAATA!!A >Ref.D.CM.01.01CM_4412HAL.AY371157 ------GCGAGAGCGTCAATATTAAGCGGGGGAAAATTGGATGCATGGGAAAAAATTCGGTTACGGCCAGGGGGAAGCAAAAAGTATAGGCTAAAACATCTAATATGGGCAAGCAATGAGCTAGAACGATTTGCACTTAATCCTGGCCTTTTAGAGACA---TCAGATGGCTGTAAACAAATACTAGGCCAGCTACAACCA---GCTCTTAAAACAGGAACAGAAGAACTTAGATCATTATTTAATGCAGTAGCAGTACTCTATTGTGTACAT---GAAAGGATAGAGGTAAAGGACACCAAGGAAGCCTTAGACAAGATAGAGGAAGAA---CAAAACAAAAGTAAG---------AAAAAAGCACAGCAAGCA------GCAGCTGACACAGGGGACAACAAA------------------CAGGTCAGCCAAAATTATCCTATAGTGCAGAACTTACAG---GGGCAAATGGTACACCAAGCCCTATCACCCAGAACCTTGAACGCATGGGTAAAAGTAATAGAGGAAAAGGCTTTCAACCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAGGATTTAAATACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGACAGGCTACATCCAGTGCAAGCAGGGCCTGTTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGATATTGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGGTGGATGACAAGTAAT---------CCACCAATCCCAGTAGGGGAAATCTATAAAAGATGGATAATCTTGGGATTGAATAAAATAGTAAGAATGTATAGCCCTGTCAGTATTTTGGATATAAGACAAGGACCAAAAGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTACACAGGAAGTAAAAAATTGGATGACAGAAACCTTGTTGGTTCAAAATGCAAACCCAGACTGTAAAACTATCTTAAAGGCGTTGGGGCCAGGGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGGCCCGGCCATAAAGCAAGAGTTTTGGCTGAGGCAATGAGC------CAAGCA------ACAGCAGGTATGAAT------GCTGCA---------ATAATGATGCAGAGGGGCAATTTTAAGGGCCCAAAGAGAATTGTTAAGTGTTTCAACTGTGGCAAAGAAGGGCACATAGCAAAAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAA---TGTGGAAGAGAAGGACACCAAATGAAAGATTGCACAGAAAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAACAAGGGAAGGCCAGGGAACTTTCTTCAGAGCAGACCA------------------------------GAGCCAACAGCCCCACCAGCA---------------------------------GAGAGCTTCGGGTTCGGGGAGGAGATAGCC---CCCTCTCAGAAACAGGAGCAG---AAAGAC------AAAGACCAGGAA---CTGTATCCTTTAACTTCCCTCAAATCACTCTTTGGCAACGACCCCTTGTCACAATAA--- >Ref.F1.FR.96.96FR_MP411.AJ249238 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCATGGGAAAGAATTCGATTAAGACCGGGGGGAAAGAAAAAATATAGAATGAAGCATCTAGTATGGGCAAGCAGGGAGTTAGAACGATTTGCAGTTGATCCTGGACTTCTAGAAACA---CCAGAAGGCTGTAAGCAAATAATAAGACAGCTACAACCA---TCCCTTCAGACAGGATCAGAAGAGCTTAGATCATTGTTCAATACAGTAGCAGTTCTCTATTGTGTACAT---CAAAAGATAGAGATAAAGGACACCAAGGAAGCTTTAGAGAAGTTAGAGGAGGAA---CAAAACAAAGGTCAG---------CAAAAGACACAGCAAGCG------GCAGCTGACAAAGGA------------------------------GTCAGTCAAAATTACCCTATAGTACAAAATCTTCAG---GGACAGATGGTACATCAGCCTATATCACCTAGAACTTTAAATGCATGGGTAAAAGTGATAGAAGAGAAGGCTTTTAGCCCAGAAGTAATACCCATGTTCTCAGCATTATCAGAAGGGGCCACCCCACAAGATTTAAACACCATGCTAAATACAGTGGGTGGACATCAAGCAGCCATGCAAATGTTAAAAGACACCATCAATGAGGAAGCTGCAGAATGGGACAGATTACATCCAGCGCATGCAGGGCCTATCCTACCAGGCCAGATGAGAGAACCTAGGGGTAGTGACATAGCTGGAACTACTAGTACCCTTCAGGAACAAATACAATGGATGACAAGCAAC---------CCACCTGTCCCAGTGGGAGACATCTATAAAAGATGGATCATCCTAGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTTAGCATTTTGGACATAAGACAAGGGCCAAAGGAACCTTTTAGAGACTATGTGGACAGGTTCTTTAAAACTCTAAGAGCTGAGCAAGCTTCACAGGAAGTAAAGAATTGGATGACAGAAAGCTTGCTGGTGCAAAATTCGAACCCAGACTGTAAGACCATCTTAAAAGCATTAGGACCAGGGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCTGGCCATAAGGCAAGGGTTTTGGCTGAGGCCATGAGC------CAAGCA------ACA---------AAT------GCAGCT---------ATAATGATGCAGAAAAGTAACTATAAGGGCCCAAGAAGATTTATTAAATGTTTTAATTGTGGCAAAGAAGGACACATAGCCAAAAATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAA---TGTGGAAAAGAAGGACATCAAATGAAAGACTGCACTGAAAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAACAAGGGGAGGCCCGGAAATTTTCTTCAGAACAGGCCA------------------------------GAGCCAACAGCCCCGCCAGCG---------------------------------GAGAGCTTCGGGTTCAAAGAGGAAATAACC---CCCTCTCCGAAGCAGGAGCAG---AAGGAC------GAGGGACAGGGACTGTATCCTCCCTTAGCCTCCCTCAAATCACTTTTTGGCAGCGACCCT!TAGTCACCATA!!A >Ref.A2.CY.94.94CY017_41.AF286237 ATGGGTGCGAGAGCGTCAATATTAAGCGGGGGAAAATTAGATGCTTGGGAGAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAGACTGAAACATTTGGTATGGGCAAGCAGGGAGCTGGAGAAATTCTCAATTAACCCTGGCCTTTTAGAAACA---CCAGAGGGATGTAGACAAATAATAAGGCAGTTACAACCA---GCTCTCCAAACAGGAACAGAAGAACTTAAATCATTATATAATACAGTAGTAGTCCTCTACTGGGTACAT---CAAAGGGTAGATGTAAAAGACACCAAGGAAGCTCTAGATAAAATAGAGGAAGAA---CAAAACAAG---------------CAGAAAACACAGCATGCA------GCAGCTGACACAGGGAACAGCAGC------------------------AGTCAAAATTATCCCATAGTGCAAAATGCACAA---GGGCAAATGGTACACCAGGCTATATCACCTAGGACGTTGAATGCCTGGGTCAAAGTAGTAGAAGAAAAGGCTTTCAGCCCAGAAGTAATACCTATGTTTACAGCATTATCAGAAGGAGCCACCCCACAAGACTTAAATACTATGCTAAACACAGTGGGGGGACATCAAGCAGCTATGCAAATGTTAAAAGATACCATCAATGAGGAAGCTGCAGAATGGGACAGGGTACATCCAGTACATGCAGGGCCTATTCCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGTTGGATGACCAGCGAT---------CCACCCATCCCAGTGGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAGACAAGGGCCAAAAGAACCCTTTAGAGATTATGTGGATAGGTTCTTTAAAACTCTAAGAGCTGAGCAAGCCACACAGGAGGTAAAAAACTGGATGACGGACACCTTGCTGGTCCAAAATGCGAACCCAGATTGTAGATCCATCTTGAGAGCATTAGGACCAGGGGCCTCATTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCCAGCCATAAAGCAAGGGTTTTGGCTGAAGCAATGAGCCATGTACAAAGT------ACA---------AAT------ACAAAC---------ATAATGATGCAGAGAGGCAATTTTAGGGGTCAAAAAAGA---ATTAAGTGTTTCAACTGTGGCAAGGAAGGACACCTAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGCTGGAAA---TGTGGAAAGGAAGGACATCAAATGAAAGATTGCACTGAGAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAACAAAGGGAGGCCAGGAAATTTTCCTCAGAGCAGAACA------------------------------GAGCCAACAGCCCCACCAGCA---------------------------------GAGAACTTGAGAATGGGGGAAGAGATAACC---TCCTCCCTGAAGCAGGAACTG---GAGACC------AGGGAACCA------TACAATCCTGCAATTTCCCTCAAATCACTCTTTGGCAACGACCCCTTGTTACAGTAA--- >Ref.H.CF.90.056.AF005496 ATGGGTGCGAGAGCGTCAGTATTAAGCGGCGGAAAATTAGATGCTTGGGAGAAAATTCGGCTAAGGCCAGGGGGAAAGAAAAAATATAGGCTAAAACATCTAGTATGGGCAAGCAGGGAGCTGGAAAGATTTGCACTTAACCCCGGCCTTTTAGAAACA---CCAGAAGGCTGTCTACAGATAATAGAACAGATACAGCCA---GCTATTAAGACAGGAACAGAAGAACTTAAATCATTATTTAATCTAGTAGCAGTCCTCTATTGCGTACAT---CGAAAAATAGATGTGAAAGACACCAAGGAGGCTTTAGATAAGATAGAGGAAATA---CAAAACAAAAGTCAG---------CAAAAAACACAGCAAGCA------GCAGCTGATAAGGAAAAAGACAAC------------------AAGGTCAGTCAAAATTATCCTATAGTACAGAATGCTCAA---GGGCAGATGGTACACCAGGCCATATCACCTAGGACCTTAAATGCATGGGTAAAAGTAGTAGAAGAAAAGGCTTTTAGCCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGACTTAAATGCTATGCTAAATACAGTGGGGGGACATCAAGCAGCCATGCAGATGTTAAAAGATACAATCAATGAGGAAGCTGCAGAATGGGACAGGGTACATCCAGTGCATGCAGGGCCTATTCCACCAGGCCAAATGAGAGAACCAAGGGGAAGCGATATAGCAGGAACTACTAGTACCCTGCAGGAACAAATAGCATGGATGACAGGCAAT---------CCAGCTATCCCAGTGGGAGACATCTATAAAAGATGGATAATCCTGGGATTAAATAAGATAGTAAGAATGTATAGTCCTGTCAGCATTCTGGACATAAAACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTTTTTAAAACTTTAAGAGCTGAGCAAGCCACACAGGATGTGAAGAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCAAATCCAGATTGCAAGACTATATTAAGAGCATTAGGACAAGGGGCTTCAATAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCTAGTCATAAAGCAAGAGTTTTGGCTGAGGCAATGAGC------CAAGTA------ACA---------AAT------ACAAATACA---GCCATAATGATGCAGAAAGGCAACTTTAAGGGCCAAAGAAAATTTGTTAAATGCTTCAACTGTGGCAAAGAGGGACACATAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAA---TGTGGAAGAGAAGGACATCAGATGAAAGACTGCACAGAGAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAGCAAAGGGAGGCCAGGAAATTTTCTCCAGAGCAGGCCA------------------------------GAACCAACAGCCCCACCAGCA---------------------------------GAGAGCTTCGGGTTCGGAGAGGAGATGACC---CCCTCTCCGAAGCAGGAGCAGCTGAAGGAC------AAGGAA------------CCTCCCTTAGCTTCCCTCAGATCACTCTTTGGCAGCGACCCCTTGTTACAGTAA--- >Ref.A2.CM.01.01CM_1445MV.GU201516 ------GCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCTTGGGAGAAAATTCGGTTAAGGCCAGGGGGAAGGAAAAAATATAGAATGAAACATTTAGTATGGGCAAGCAGGGAGCTGGAAAAATACTCAATCAACCCTGGTCTTTTAGAAACA---TCGGAAGGATGTAAACAAATAATAAGGCAGTTACATTCA---GCTCTCCCAGTAGGAACAGAAGAACTTAAATCACTATATAATACAATAGCAGTCCTCTACTATGTACAT---CAAAAAATAGAGGTAAAAGACACCAAGGAAGCCCTAGATAAATTAGAGGAGGAG---CAAAACAAATACAAG---------CAGAAGACACAGCAGGCA------GCAGCTGCCACAGGAAATAGCAGC------------------------AGTCAGAATTATCCCATAGTGCAAAATGCACAA---GGGCAAATGGTGCACCAGGCCATATCGCCTAGGACTTTGAATGCATGGGTCAAAGTAGTAGAAGAAAAAGCTTTCAGCCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAATACTATGCTAAACACAGTGGGGGGACATCAAGCAGCTATGCAAATGTTAAAGGATACCATCAATGAGGAAGCTGCAGAATGGGACAGGGTACATCCAGTACATGCAGGGCCTATTCCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACCAGCAAC---------CCACCTATCCCAGTGGGAGAAATCTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAGACAAGGGCCCAAAGAACCCTTTAGAGACTATGTAGATAGGTTCTTTAAAACTCTCAGAGCTGAACAAGCTACACAGGATGTAAAAAATTGGATGACAGACACCTTGCTGGTCCAAAATGCGAACCCAGATTGTAAAACTATCCTGAGAGCGTTAGGACCAGCGGCTACATTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCCGGCCATAAAGCAAGGGTCTTGGCTGAAGCAATGAGC------CAAATACACAGTACA---------AAT------CAAAAT---------GTAATGATGCAGAGAGGCAATTTTAGAGGTCCAAAAAGA---ATTAAGTGTTTCAACTGTGGCAAGGAAGGACACCTAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGTTGCTGGAAA---TGTGGGAAGGAAGGACATCAAATGAAAGATTGCACTGAGAGACAGGCTAATTTTTTAGGGAAAATCTGGCCTCCCAACAAAGGGAGGCCAGGAAACTTTCCCCAGAGCAGAACA------------------------------GAGCCAACAGCCCCGCCAGCA---------------------------------GAGAACGTTGGAATGGGGGAAGAGATAGCT---TCCTCGTCGAAGCAGGAACTG---AGAAAC------AGGGAACAA------CACACTCCTACAATTTCCCTCAGATCACTCTTTGGCAACGACCCCTTGTCACAGTAA--- >Ref.A1.AU.03.PS1044_Day0.DQ676872 ATGGGTGCGAGAGCGTCAATATTAAGCGGGGGAAGATTAGATGCATGGGAGAAAATTCGGCTAAGGCCAGGGGGAAAGAAAAAATATAGACTAAAACATCTAGTATGGGCAAGCAGGGAGCTGGAGAGATTCGCACTTAAYCCTRGCCTTTTAGAATCA---GCAGAAGGATGTCAACAAATAATGGAACAGTTACAACCA---GCTCTYAAGACAGGAWCAGAAGAAATTAAATCATTATTTAATACAGTAGCAACCCTCTATTGTGTACAT---CAAAGGATAGATGTAAAAGACACCAAGGAAGCTYTAGATAAAATAGAGGAAATA---AAAAATAAGAGCAAG---------CAAAGGACTCAACAGGCA------GCAGCTGACACAGGAAACAGCGGC------------------AAGGTCAGCCAAAATTACCCTATAGTGCAAAATGCACAG---GGGCAAATGATACAYCAAAACTTGTCACCTAGAACTTTAAATGCATGGGTAAAAGTAATAGAAGAAAAGGCTTTTAGTCCAGAAGTGATACCCATGTTCTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAATGTAATGCTGAACATAGTGGGGGGACACCAGGCAGCTATGCAAATGTTAAAAGACACCATCAATGAAGAAGCTGCAGAATGGGACAGGTTACATCCAGTACATGCAGGGCCTATTCCACCAGGCCAGATAAGAGAACCAAGGGGAAGTGACATAGCAGGAGCTACTAGTACCCCTCAAGAACAATTACAATGGATGACAGGCAAC---------CCACCTATCCCAGTGGGAGACATCTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACTAGCATTTTGGATATAAGACAAGGGCCAAAAGAATCCTTCAGAGACTATGTAGATAGGTTCTTTAAAGCTCTTAGAGCTGAGCAAGCTACACAGGAGGTAAAAAGTTGGATGACAGAGACATTACTGGTCCAAAATGCAAATCCAGATTGTAAGTCCATTCTAAAAGCATTAGGATCAGGAGCTACATTAGAAGAAATGATGACAGCATGCCAGGGAGTGGGAGGACCCAGCCATAAGGCAAGGGTTTTGGCTGAAGCAATGAGT------CAAGCA------CAA---------CAA------ACAAGC---------ATAATGATGCAGAGAGGCAACTTTAGGGGCGGCCAGAAAAGGATTAAGTGTTTTAACTGTGGCAAAGAAGGACACCTAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAA---TGTGGGAAGGAGGGACACCAAATGAAAGACTGCACTGAAAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAGCAAGGGGAGGCCAGGAAATTTCCCTCAGAGCAGACCA------------------------------GAGCCAACAGCCCCACCAGCG---------------------------------GAGCTCTTTGGGATGGGGGAAGAGATAACC---TCCCCTCCGAAGCAGGAGCAG---AAGGAC------AAGGAACAG------GTCCCACCCTTAGTTTCCCTCAAATCACTCTTTGGCAACGACCCATCGTCACAGTAA--- >Ref.J.SE.93.SE9280_7887.AF082394 ATGGGTGCGAGAGCGTCAATATTAAGTGGGGGAAAATTAGATGATTGGGAAAAAATTCGGTTGAGGCCAGGGGGGAAGAAAAAATATAGGATAAAGCATCTAGTATGGGCAAGCAGGGAGCTGGACAGATTTGCACTTAACCCTGGCCTTCTAGAGTCA---GCAAAAGGCTGTCAACAAATACTAGTACAGCTCCAACCA---GCTCTCCAGACAGGAACACAAGAAATTAAATCATTGTATAATACAGTAGCAACCCTCTATTGCGTACAT---CAGAGGATAGAAATAAAAGACACCATGGAAGCTTTAGAGAAGATAGAGGAAATT---CAAAACAAGAACAAA---------CAGCAGGCACAGAAAGCA------GAAACTGACAAAAAAGACAACAGT------------------CAGGTCAGTCAAAATTATCCTATAGTGCAGAATCTGCAA---GGGCAACCGGTACACCAGGCCCTATCACCTAGAACTTTAAATGCATGGGTAAAAGTGATAGAAGAAAAAGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCGCAAGATTTAAATACCATGCTAAACACAATAGGGGGACACCAAGCAGCTATGCAAATGTTAAAAGATACTATCAATGAGGAAGCTGCAGAATGGGACAGGGTACATCCAGTACATGCAGGGCCTATTGCACCAGGCCAGGTGAGAGAACCAAGGGGAAGTGATATAGCAGGAACTACTAGTACCCTCCAGGAACAAATAGGATGGATGACAGGCAAT---------CCACCTATCCCAGTAGGAGAGATTTATAAAAGATGGATAATTCTGGGACTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGTATTTTGGATATAAGACAAGGACCAAAAGAACCTTTTAGAGACTATGTAGACAGGTTCTTTAAAGCTCTAAGAGCTGAGCAAGCTACACAGGATGTAAAAAATTGGATGACAGATACCTTGCTGGTCCAAAATGCAAATCCAGATTGCAAGACCATTTTAAAAGCATTAGGATCAGGAGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCTGGTCATAAGGCGAGAGTTTTGGCTGAAGCAATGAGC------CAAGTG------ACC---------AAT------ACCAAC---------ATAATGATGCAAAGAGGTAACTTTAGGGACCATAAAAGAATTGTTAAGTGTTTCAATTGTGGCAAACAAGGACACATAGCAAAAAACTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAA---TGTGGAAAGGAAGGACACCAAATGAAAGACTGCACTGAGAGACAGGCTAATTTTTTAGGGAAGATTTGGCCTTCCAGCAAAGGGAGGCCAGGGAACTTTCTCCAGAGCAGACCA------------------------------GAGCCAACAGCCCCACCAGCA---------------------------------GAGAGCCTCGGGCTCGGAGAGGAGATC------CCCTCCCCGAAACAGGAGCCG---AAGGAC------AAGGAACTG---------TATCCTCTAACTTCCCTCAAATCACTCTTTGGCAGCGACCCCTTGTCACAATAA--- >Ref.F2.CM.95.95CM_MP257.AJ249237 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCATGGGAAAAAATTCGGTTAAGGCCGGGGGGGAAGAAAAAATATAGGCTGAAACATATAGTATGGGCAAGCAGGGAGCTAAAACGATTTGCACTTAATCCTGGCCTTTTAGAGACA---ACAGAAGGCTGTAAGAAAATAATAGGACAACTACAACCA---TCCCTTCAGACAGGGTCAGAGGAACTGAAATCATTATTTAACACAATAGTAGTTCTCTATTATGTACAT---CAAAAGATAGAGGTAAGAGACACCAAGGAAGCTTTAGATAAGCTACAGGAAGAA---CAAGACAAACATCAG---------CAAAAAACACAACAAGCA------ACGGCTGACAAAGGGGTCAGTAAA------------------GGGGTCAGTCAAAATTACCCTATACTACAAAATCTTCAG---GGGCAAATGGTACACCAGAGTCTATCACCTAGAACTTTAAATGCATGGGTAAAAGTAATAGAAGAGAAGGCTTTCAGCCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGGGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACCATCAATGAGGAAGCTGCAGAATGGGACAGGTTACATCCAGTGCATGCAGGACCTATCCCACCAGGTCAGATGAGAGAACCAAGGGGAAGTGATATAGCAGGAACCACTAGTACCCTTCAGGAACAAATAGCATGGATGACAAGCAAC---------CCACCTGTCCCAGTAGGAGAAATCTATAAAAGATGGATAATCCTAGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAAACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTCTTTAAAACTCTAAGAGCTGAGCAAGCCACGCAGGAAGTAAAAGGCTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACCATTTTAAAAGCATTGGGGCCAGGGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGTGTGGGAGGACCTAGCCATAAAGCAAGAATTTTGGCTGAGGCAATGAGC------AAAGCA------ACA---------GGT------GCAGCC---------ATAATGATGCAGAAGAGCAACTTTAAGGGCCAAAGAAGAATTGTTAAGTGTTTTAACTGTGGCAAAGAAGGACATATAGCTAGAAATTGCAGGGCCCCTAGAAAAAGGGGCTGCTGGAAA---TGTGGACAGGAAGGACACCAAATGAAAGACTGCACTGAGAGACAGGCTAATTTTTTAGGGAAAATGTGGCCTTCCAACAAGGGGAGGCCCGGAAATTTTCTTCAGAACAGACCA------------------------------GAGCCAACAGCCCCGCCAGCA---------------------------------GAGAGCTTCGGGTTCGGGGAGGAGATAGCT---CCCTCCCCGAAGCAGGAGCAG---AAAGAC------AAGGAACAG------GTTCCTCCCTTGATTTCCCTCAAATCACTCTTTGGCAGC!GACCAGTAGTCACAATA!!A >Ref.F2.CM.95.95CM_MP255.AJ249236 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCATGGGAAAAAATTCGGTTAAAGCCGGGGGGAAAGAAAAGATATAGGCTAAAACATCTAGTATGGGCAAGCAGGGAACTAGAACGATTTGCACTTAATCCTAGCCTTTTAGAAACA---ACAGAAGGCTGTAAGAAAATAATAGGACAATTACAATCA---TCCCTTCAGACAGGATCAGAAGAGCTTAAATCACTATACAATGCAGTAGTAGTTCTCTATTATGTACAT---CAAAGGATAGATGTAAGAGACACCAAGGAAGCTTTAGATAAGCTACAGGAAGAA---CAAGATAAAAGTCAG---------CAAAAGGAACAACAAAAG------GCGGCTGACAAAGAG------------------------------GTCAGTCAAAATTACCCTATAGTGCAGAATATTCAG---GGGCAAATGGTACACCAGGCTCTATCACCTAGAACTTTAAATGCATGGGTAAAAGTAATAGAAGAGAAGGCTTTCAGTCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGGGCCACCCCACAAGATTTAAATACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACTATCAATGAGGAGGCTGCAGAATGGGACAGGTTACATCCAGTGCATGCAGGGCCTATCCCACCAGGGCAGATGAGAGAACCTAGGGGAAGTGATATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAACATGGATGACAGGCAAC---------CCACCCGTCCCAGTAGGAGAAATCTATAAAAGATGGATAATCCTAGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAAACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTCTTTAAAACTCTAAGAGCTGAACAAGCTACACAGGAGGTAAAAAACTGGATGACAGAAACCTTGTTGGTCCAAAATTCGAACCCAGATTGTAAGACAATTTTAAAAGCATTGGGACCAGGGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCTGGCCATAAAGCAAGAATTCTGGCTGAGGCAATGAGC------AAAGCA------ACA---------AGT------ACAGCC---------ATAATGATGCAGAAAAGCAACTTTAAGGGCCAAAAAAGAATTGTTAAGTGTTTCAACTGTGGCAAAGAAGGACATATAGCTAGAAATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAA---TGTGGAAAGGAAGGACACCAAATGAAAGACTGCACTGAAAGGCAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAACAGGGGGAGGCCAGGAAATTTTCTTCAGAACAGACCA------------------------------GAGCCAACAGCCCCGCCAGCA---------------------------------GAGAACTTCGGGTTCGGAGAGGGGATAACC---CCCTCCCCGAAGCAGGAGCAG---AAAGGC------GAGGAACAG------GCTCCTCCCTTAGTTTCCCTCAAATCACTCTTTGGCAGCGACCCT!!TAGTCGCAAT!AA >Ref.C.BR.92.BR025_d.U52953 ATGGGTGCGAGAGCGTCAATATTAAGAGGCGGAAAATTAGATGCTTGGGAAAGAATTAAGTTAAAGCCAGGGGGAAAGAAACACTATATGATGAAACACCTAGTCTGGGCAAGCAGGGAGCTGGAAAGATTTGCACTTGACCCTGGCCTTTTAGAGACA---TCCGAAGGCTGTAAACAAATAATGAAACAGCTACAACCA---GCTCTTCAGACAGGAACAAAGGAACTTATATCATTACATAATACGGTTGCAACTCTCTATTGTGTACAT---GAAAAGATAGATGTACGAGACACCAAGGAAGCCTTAGACAAAATAAAGGAAGAA---CAAAACAAAAGTCAG---------CAAAAAACACAGCAGGCA---GAAGCGGCTGACAAAGGA---------------------------AAGGTCAGTCAAAATTATCCTATAGTACAGAATCTCCAA---GGGCAAATGGTACACCAGCCCATATCAGCTAGAACTTTGAATGCGTGGGTAAAGGTAGTAGAGGAGAAGGCTTTCAGCCCAGAGGTAATACCCATGTTTACAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGTTAAATACAGTGGGGGGACACCAAGCAGCCATGCAAATGTTAAAAGATACCATCAATGAGGAGGCTGCAGAATGGGATAGATTACATCCAGTGCATGCAGGGCCTGTCGCACCAGGCCAAATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACCAGTACCCTTCAGGAACAAATAACATGGATGACAAATAAC---------CCACCTGTCCCAGTAGGAGACATCTATAAAAGATGGATAATTCTGGGGTTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAAACAAGGGCCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTTTAAAACTCTAAGAGCAGAGCAAGCTACCCAAGATGTAAAAAATTGGATGACAGATACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACCATTTTAAGAGCATTAGGGCCAGGGGCTTCATTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCTGGCCACAAAGCAAGAGTGTTGGCTGAGGCAATGAGC------AAAGTA------AAC---------AAT------ACAAAC---------ATAATGATGCAAAGAAGCAATTGTAAAGGCCCTAAAAGAACTATTAAATGCTTCAACTGTGGCAAGGAAGGGCACTTAGCCAGAAATTGCAGGGCTCCTAGGAAAAAAGGCTGTTGGAAA---TGTGGAAAAGAAGGACACCAAGTGAAAGACTGTACTGAGAGGCAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCCACAGGGGGAGGCCAGGAAATCTTCTTCAGAACAGAACA------------------------------GAGCCAACAGCCCCACCAGAA---------------------------------GAGAGCTTCAGGTTTGGGGAAGAGACAACAACTCCCTCTCGGAAGCAGGAGACG---ATAGAC------AAGGAACTG------------CCCTTAACTTCCCTCAAATCACTCTTTGGCAGCGACCCCTTGTCAACATAA--- >Ref.G.KE.93.HH8793_12_1.AF061641 ATGGGTGCGAGAGCSTCASTATTAAGCGGGGGAAAATTAGATGCATGGGAAAAAATTCGSCTGACGCCAGGGGGAAAGAAAAAATACAGACTGAAACATCTAGTATGGGCAAGCAGAGAGATGGAGAGATTTGCACTTAACCCTGGCCTTTTAGAAACA---GCAGAAGGTTGTCAACAAATAATGAGCCAGTTGCAACCA---GCTATCCAMACAGGAACAGAGGAGATTAAATCATTATTTAATACAGTAGCAACCCTCTATTGTGTACATCCC---AAGATAGAGGTAAAGGACACCAAAGAAGCTCTAGAGGAAGTAGAAAAGATA---CAAAAGAAAAGTCAG---------CAAAAAATACAGCAGGCA------GCAAGGGATGAAGGAAACAGCAGC------------------CAAGTCAGCCAAAATTATCCTATAGTGCAGAACGCACAA---GGACAGATGGTACACCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAAAAGGCCTTCAGTCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAATACCATGCTAAACACAGTGGGGGGGCATCAAGCAGCTATGCAAATGCTAAAAGATACTATCAATGAGGAAGCTGCAGAGTGGGACAGAATACATCCACCACAGGCAGGGCCTATTCCACCAGGCCAAATAAGAGAACCAAGGGGAAGTGATATAGCAGGAACCACTAGTAACCTGCAGGAACAAATAAGATGGATGACCAGCAAC---------CCACCTATCCCAGTGGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAGACAAGGGCCAAAAGAACCCTTTAGAGATTATGTAGACAGGTTCTTTAAAACTTTAAGAGCTGAGCAAGCTACACAGGAAGTAAAAGGCTGGATGACAGACACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATCTTAAGAGCATTAGGACCCGGAGCTACACTAGAAGAAATGATGACAGCATGCCAGGGAGTGGGAGGACCCGGCCATAAAGCAAGAGTGTTAGCTGAGGCAATGAGC------CAGGCA------ACA---------GGT------GCAGCAGCA---GCCATAATGATGCAGAAAAGCAACTTTAAGGGCCCGAAAAGAAATATCAAGTGTTTCAATTGTGGCAAGGAAGGACACTTAGCCAGAAATTGCAGGGCCCCTAGAAAAAAGGGCTGCTGGAAA---TGTGGAAAGGAGGGACATCAAATGAAAGACTGCACGGAAAGACAGGCTAATTTT!TAGGGAAAATTTGGCCTTCCAACAAGGGGAGGCCAGGGAATTTTCTTCAGAACAGGCCA------------------------------GAGCCAACAGCCCCACCCGCA---------------------------------GAGAGCTTCGGGTTCGGAGAGGAAATAGCC---CCCTCCCCGAAGCCAGAGCCG---AAGGAA------AAGGAGATA---------CATCCCTTAGCTTCCCTCAAATCACTCTTTGGCAGCGACCCC!TAGTCACAGTA!!A >Ref.A2.CD.97.97CDKTB48.AF286238 ATGGGTGCGAGAGCGTCAGTATTGAGCGGCGGAAAATTAGAAGCTTGGGAGAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAGACTGAAACATTTAGTATGGGCAAGCAGGGAGCTGGAAAAATTCTCAATCAACCCCAGCCTTTTAGAAACA---GAAACAGGATGTAGACGAATATTTGGGCAATTACAACCA---GCTCTCGAGACAGGAACAGAAGAACTTAGATCATTATATAATACAATAGCAGTCCTCTACTTTGTTCAT---CAAAAGATAGAGGTAAAAGACACCAAGGAAGCTCTAGATAAAATAGAGGAAGAA---CAAAACAAATGCAAG---------CAGAAGACACAGCAGGCA------GCAGCTGACACAGGAAGCAGCAGCAGTCAAAATTACAGAGGTAGCAGCAGTCAAAATTACCCTATAGTGCAAAATGCACAA---GGGCAAATGGTACACCAGGCCGTGTCACCTAGGACTTTGAATGCATGGGTCAAAGTAGTTGAAGAGAAGGCTTTTAGCCCAGAAGTAATACCCATGTTTACAGCATTATCAGAAGGAGCCACCCCACAAGACTTAAATACTATGCTAAACACAGTGGGGGGACATCAAGCAGCTATGCAAATGTTAAAAGATACCATCAATGAGGAAGCTGCAGAATGGGACAGGTTACATCCAGTACAGGCAGGGCCTATTCCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCGGGAGCTACTAGTAACCTTCAGGAACAAATAGGATGGATGACCAGCAAC---------CCACCTATTCCAGTGGGAGAAATCTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAAACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGATAGGTTCTTTAAAACTCTCAGAGCTGAGCAAGCTACACAGGAGGTAAAAAATTGGATGACAGACACCTTGCTGGTCCAAAATGCAAACCCAGATTGTAAATCCATCTTGAGGGCATTAGGACCAGGGGCTACATTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCCGGCCATAAAGCAAGGGTTTTAGCTGAAGCAATGAGC------CAAGTA------CAA---------AAT------ACAAAC---------ATAATGATACAGAGAGGCAATTTTAAGGGTCAAAAAAGA---ATTAAGTGTTTCAACTGTGGCAAGGAAGGACACCTAGCTAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGCTGGAAA---TGTGGGAAGGAAGGACATCAAATGAAAGACTGCACTGAGAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAACAAAGGGAGGCCAGGGAATTTTCCTCAGAGCAGGACA------------------------------GAGCCAACAGCCCCACCAATG---------------------------------GAG---------------GAAGAGATAACC---TCCTCGCTGAAGCAGGAGAAC---AGGGAG------CCGTCCACC------------CCTGCAATTTCCCTCAAATCACTCTTTGGCAACGACCTCTTGTCACAGTGA--- >Ref.G.BE.96.DRCBL.AF084936 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCTTGGGAGAAAATTCGGTTGAGGCCAGGGGGAAAGAAAAGATATAGAATGAAACATTTAGTATGGGCAAGCAGGGAGCTGGACAGATTTGCACTTAACCCTGGCCTTTTAGAAACA---GCAGAAGGTTGTCAAAAAATAATGGCACAGTTGCAACCA---GCTCTCCAAACAGGAACAGAGGAGATTAAATCACTATTTAATACAGTAGCAACCCTCTATTGTGTACAT---CAAAAGATAGAGGTAAGAGACACCAAAGAGGCTCTAGAGGAAGTGGAAAAGATA---CAAAAGAAGAGTCAG---------CAAAAAGAAAACAGCAGC------AGC---------------------------------------CAAGTCAGTCAAAATTACCCTATAGTGCAGAATGCACAA---GGGCAAATGGTACACCAGGCCATATCACCTAGAACTTTGAATGCATGGGTAAAAGTAGTAGAAGAAAAGGCCTTCAGTCCAGAAGTAATACCCATGTTTACAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAATACCATGCTAAATACAGTGGGGGGGCATCAAGCAGCTATGCAAATGTTAAAGGAGACTATCAATGATGAAGCTGCAGAATGGGACAGGCTACATCCACAGCAGGCAGGGCCTATTGCACCAGGCCAGATAAGGGACCCAACGGGAAGTGATATAGCAGGAGCTACTAGTACCCTGCAGGAACAGATAAGATGGATGACCAGCAAC---------CCACCTGTCCCAGTGGGAGAAATTTATAAAAGATGGATAATCCTGGGGTTAAATAAAATAGTAAGAATGTACAGCCCTGTCAGCATTTTGGACATAAGACAGGGGCCAAAAGAACCCTTTAGAGATTATGTGGATAGATTCTTTAAAACCCTGAGAGCTGAGCAAGCTACACAGGAAGTAAAAAGCTGGATGACAGACACCTTGTTGATCCAAAATGCAAACCCAGATTGTAAGATCATCTTAAAAGGATTAGGACAAGGAGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCCAGCCATAAAGCAAGAGTTTTAGCTGAGGCAATGAGC------CAGGCA------TCA---------GGT------GCAGCAGCA---GCCATAATGATGCAGAAAAGCAATTTCAAGGGCCCAAGAAGAACAATTAAATGTTTCAACTGTGGCAAGGAAGGACATCTAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAA---TGTGGAAAGGAGGGACATCAAATGAAAGAATGCACAGAAAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAACAAGGGGAGGCCAGGGAATTTCCTTCAGAACAGGCCA------------------------------GAGCCAACAGCCCCACCCGCA---------------------------------GAGAACTTCGGGTTCGGGGAGGAGATAGCC---CCCTCCCCGAAGCAGGAGCAG---AAGGAA------AAGGAACTA---------TATCCTCTATCTTCCCTCAAATCACTCTTTGGCAAC!GACCAATAGTCAAAGTA!!A >Ref.K.CD.97.97ZR_EQTB11.AJ249235 ATGGGTGCGAGAGCTTCAGTATTAAGCGGGGGAAAATTAGACAAATGGGAAAAAATTCAGTTACGGCCAGGGGGAAAGAAAAAATACAGGCTAAAACATCTAGTATGGGCAAGCAGGGAGCTAGAACGATTTGCACTTAACCCTAACCTTTTAGAGACA---GTAGAAGGCTGTCGGCAAATAATAAGACAACTACAACCA---TCCCTTCAAACAGGCTCGGAAGAGCTTAGATCACTATTTAATACAGTAGCAACCCTCTATTGGGTGCAT---CAAAGTATACAGGTAAGGGACACCAAGGAAGCCTTAGACAAACTAGAGGAAGAA---CAAAACAGAACTCAG---------CAAAAGACACAGCAAGGA------AAAGCTGACAAAGGG------------------------------GTTAGTCAAAATTACCCTATAGTACAGAATCTTCAG---GGGCAAATGGTACACCAGGCCCTATCACCTAGAACTTTAAATGCATGGGTTAAAGTAATAGAAGAGAAGGCTTTCAGCCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACTCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACTATCAATGAGGAAGCTGCAGAATGGGACAGGATGCACCCAGTGCAAGCAGGGCCTATCCCACCAGGCCAAATAAGAGAACCTAGGGGGAGTGATATAGCAGGAACTACTAGCACTCTTCAGGAACAAATAACATGGATGACAAGCAAC---------CCACCTATCCCAGTGGGAGAAATCTATAAAAGATGGATAATCCTGGGGTTAAATAAAATAGTGAGAATGTATAGCCCTGTCAGCATTTTGGACATAAGACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGATAGGTTCTTTAGAGTTCTAAGAGCTGAACAAGCCACACAGGAAGTAAAAAATTGGATGACAGAAACCCTGTTGGTCCAAAACGCAAACCCAGATTGTAGGACCATTTTAAAGGCGTTGGGATCAGGGGCTACATTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGGCCTGGCCATAAAGCAAGGGTTTTGGCTGAGGCAATGAGC------CAGGTA------ACA---------AAT------TCAGCC---------GTAATGATGCAGAGAGGCAACTTTAAGGGTCAAAGAAGAATTATTAAGTGCTTCAACTGTGGCAAAGAAGGACACCTAGCCAGAAATTGTAGGGCCCCTAGAAAAAAGGGCTGTTGGAAA---TGTGGGAAAGAAGGACATCAGATGAAAGACTGTTCTGAGAGACAGGCTAATTTTTTAGGGAAGTTCTGGCCTCTCAACAAAGAGAGGCCAGGAAATTTTCTTCAGAACAGACCA------------------------------GAGCCAACAGCCCCACCAGCA---------------------------------GAGAGCTTTGGGTTCGGGGAGAAGATAACC---CCCTCTCTGAGACAGGAAATG---AAAGAT------CAGGAACAG------GGTCCTCCTTTAACTTCCCTCAAATCACTCTTTGGCAGCGACCCGTTGTCACAGTAA--- >Ref.D.TZ.01.A280.AY253311 ------GCGAGAGCGTCAGTATTAAGCGGGGGACAATTAGATGCATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATCAACTAAAACATATAGTATGGGCAAGCAGGGAGTTAGAACGATTTGCACTTAATCCTGGCCTTTTAGAGACA---TCCGAAGGCTGTAAACAAATC!TA---------CAACCA---GCTATTCAGACAGGATCAGAAGAACTTAAATCATTATTTAATACAGTAGCAACCCTCTATTGTGTGCAT---AGAAAGATAGAGGTAAAAGACACCAAGGAAGCTTTAGAAAAATTAGAGGAAGAG---CAAACCAAAAGTAAG---------AAAAAGGCACAGCAAGCA------ACAGCTGACACAGGAAGCAGCAGC------------------CAGGTCAGCCAAAATTATCCTATAGTGCAAAACCTACAG---GGGCAAATGGTACACCAGGCCATATCACCTAGAACCTTGAACGCATGGGTAAAAGTAATAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACAATGCTAAACACAGTGGGGGGACATCAAGCAGCTATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGGCTACATCCAGTGCATGCAGGGCCTATTGCACCAGGACAGATGAGAGAACCAAGGGGAAGTGATATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGCATGGATGACAAATAAT---------CCACCTGTCCCAGTAGGAGAAATATATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTTAGCATTTTGGACATAAGACAAGGACCAAAGGAGCCCTTTAGGGACTATGTAGATCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAAGATGTAAAAAATTGGATGACTGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAAACTATCTTAAAAGCATTGGGACCAGCGGCTACATTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGGGGACCCAGTCATAAGGCAAGAGTTCTAGCTGAGGCAATGAGC------CAAGCA------ACA---------AAT------GTAAATGCT---GCCATAATGATGCAGAGAGGTAATTTTAAGGGCCCAAGGAAAATCATTAAGTGTTTCAACTGTGGCAAAGAAGGACACATAGCAAAAAATTGCAGGGCCCCAAGAAAAAAGGGCTGTTGGAAA---TGTGGAAAGGAAGGACACCAAATGAAAGATTGCACTGAAAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCCACAAAGGAAGGCCAGGGAACTTCCTTCAGAGCAGACCA------------------------------GAGCCAACAGCCCCACCAGCA---------------------------------GAGATCTTCGGGTTTGGGGAGGAGATAAAA---CCCTCTCAGAAACAGGAGCAG---AAAGACAAGGACAAGGAACTG---------TATCCTTCAGCTTCCCTCAAATCACTCTTTGGCAACGACCCCTTGTCACAATAA--- >Ref.F2.CM.02.02CM_0016BBY.AY371158 ------GCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGACTGGGAGAAAATTCGGTTAAGGCCGGGAGGGAAGAAAAAATATAGGCTAAAACATATAGTATGGGCAAGCAAGGAGCTAGAACGATTTGCACTTAATCCTGGCCTTTTAGAGACA---ACAGAAGGCTGTAAACAAATAATAGGACAACTACAA---TCATCCCTTCAGACAGGATCAGAAGAGATTAAATCATTATATAACACAGTAGCAGTCCTCTATTATGTACAT---CAAAAGATACAAATAAGAGACACCAAGGAAGCTTTAGATAAGCTACAGGAAGAA---CAAGACAAATATCAG---------CAAAAAACACAACCAGCA------GCGGCTGATAAAGGG------------------------------GTCAGTCAAAATTACCCTATAGTACAGAATCTTCAG---GGGCAAATGGTACATCAGGCTATATCACCTAGAACTCTAAATGCATGGGTAAAAGTAATAGAAGAGAAGGCTTTCAGCCCAGAAGTCATACCCATGTTTTCAGCATTATCAGAAGGGGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTAGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACCATCAATGAGGAAGCTGCAGAATGGGACAGGTTACATCCAGTGCAGGCAGGACCTATCCCACCAGGTCAGATAAGAGAACCTAGGGGAAGTGATATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGCATGGATGACAAGCAAC---------CCACCTGTCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTAGGATTAAATAAAATAGTAAGAATGTATAGCCCTGTCAGCATTTTGGACATAAGACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGGTTCTTTAAAACTCTAAGAGCTGAGCAAGCTACACAGGAAGTAAAAGGCTGGATGACAGACACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACCATTTTAAAAGCACTAGGACCAGGGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCTGGCCATAAAGCAAGAATTTTGGCTGAGGCAATGAGC------CAAGTA------ACA---------GCT------ACATCC---------GTACTGATGCAGAAAAGCAACTTTAAGGGCCAAAAAAGAATTGTCAAGTGTTTCAACTGTGGCAAAGAAGGACATATAGCTAAAAATTGCAGGGCCCCTAGAAAAAGGGGCTGTTGGAAA---TGTGGAAAGGAAGGACACCAAATGAAAGACTGCACTGAAAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAACAAAGGGAGGCCTGGGAATTTCATTCAGAGCAGACCA------------------------------GAGCCAACGGCCCCGCCAGCA---------------------------------GAGGGCTTCGGGTTCGGAGAAGAGATAACT---CCCTCCCCGAAGCAGGAGCAG---AAAGAC------AAGGGACTG------TATCCTCCCTTGACTTCCCTCAAATCACTCTTTGGCAACGACCCG!TAGTCACAATA!!A >Ref.F1.BE.93.VI850.AF077336 ATGGGTGCGAGAGCGTCAATATTAAGCGGGGGAAAATTAGATGAATGGGAAAAAATTCAGTTAAGGCCGGGGGGAAAGAAAAGATATAAAATGAAACATCTAATATGGGCAAGCAGGGAGCTAGAACGATTTGCACTTGATCCTGGCCTTCTAGAAACA---TCAGAAGGCTGTCAAAAAATAATAAGACAGCTACAACCA---TCCCTTCAGACAGGATCAGAAGAGCTTAAGTCATTATTTAATACAGTAGCAGTCCTCTATTATGTACAT---CAAAGGGCAGGGGTAACAGACACCAAGGAAGCTTTAGACAAGCTAGAGGAAGAA---CAAAACAAAAGTCAG---------CAAAAGACACAGCAAGCG------GCAGCTGACAAAGGG------------------------------GTCAGTCAAAATTACCCTATAGTACAGAATCTTCAG---GGACAAATGGTACACCAGTCTCTATCACCTAGAACTTTAAATGCATGGGTAAAGGTGATAGAAGAGAAGGCTTTTAGCCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGGGCCACTCCCACAGATTTAAACACCATGCTAAATACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGACACCATCAATGAGGAAGCTGCAGAATGGGACAGATTACATCCAGTGCATGCAGGGCCTGCCCCACCAGGCCAGATGAGGGAACCTAGGGGGAGTGATATAGCTGGAACTACTAGTACCCTTCAGGAACAAATACAATGGATGACGGGCAAC---------CCACCTGTCCCAGTGGGAGACATCTATAAAAGATGGATCATCCTAGGATTAAATAAAATAGTAAGAATGTATAGTCCTGTCAGCATTTTGGACATAAAACAAGGGCCAAAAGAACCCTTTAGAGACTATGTAGACAGATTCTTTAAAGTCCTAAGAGCTGAGCAAGCTTCACAGGACGTAAAGGGTTGGATGACAGACACATTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACCATTTTAAAAGCATTGGGAACAGGGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCTAGCCATAAGGCAAGAGTTTTGGCCGAGGCAATGAGT------CAAGCA------------------AAT------TCAGCC---------ATAATGATGCAGAAAAGTAATTTTAAGGGCCAAAGAAGAGTTGTTAAATGTTTTAATTGTGGCAAAGAAGGACACATAGCCAGAAATTGCAGGGCCCCTAGAAAAAAGGGCTGTTGGAAA---TGTGGAAGAGAAGGACACCAAATGAAAGACTGCACTGAAAGACAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAACAAGGGGAGGCCCGGAAATTTCCTTCAGAGCAGACCA------------------------------GAGCCAACAGCCCCACCAGCA---------------------------------GAGAGCTTCGGGTTCAGAGAGGAGATAACC---CCCTCTCCGAAGCAGGAGCAG---AAAGAC------GGGGAACTG------TACCCTCCCTTAGCTTCCCTCAAATCACTCTTTGGCAACGACCCT!TAGTCACAATA!!A >Ref.B.NL.00.671_00T36.AY423387 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATAGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAGATATAAATTAAAACATATAGTATGGGCAAGCAGAGAGCTAGAACGATTCGCAGTTAATCCTGGCCTTTTAGAGACA---TCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCA---GCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATTTAATACAGTAGCAACCCTCTATTGTGTGCAT---GCAAGGATAGAGGTAAAAGACACCAAGGAAGCTTTAGAAAAAATAGAGGAAGAA---CAAAACAAAAGTAAGAAACGGGCACAGCAAGCACAGCAAGCA------GAAGCTGACGCAGGAAAAAACAAC------------------CCGGTCAGCCAGAATTACCCTATAGTGCAGAATCTCCAA---GGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCCTTCAGCCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGATTGCATCCAGTGCATGCCGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAAT---------CCACCTATCCCAGTAGGAGAAATATATAAGAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAAACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGATCGGTTCTATAAAACTTTAAGAGCTGAGCAAGCCTCACAGGAAGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATTCGAACCCAGATTGTAAAACTATTTTAAAAGCATTGGGACCAGCAGCTACACTAGAAGAAATGATGACCGCATGTCAGGGAGTAGGGGGACCCGGCCATAAAGCGAGAGTTTTGGCTGAGGCAATGAGC------CAAGTA------ACA---------AGT------GCACCT------GCCATAATGATGCAGAGAGGCAATCATAGAAACCAAAGAAGGACTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACATAGCCAGAAATTGCAGGGCCCCTAGNAAAAAGGGCTGTTGGAAA---TGTGNAAAGNAAGGACACCAAATGAAAGATTGTACTNAGAGACAGGCTANTTTTTTAGGGAAGATTTGGCCTTCCCACAAGGGGAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCTTCTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAA---------------------------------GAGAGCTTCAGGTTTGGGGAAGAGACAACAACTCCCTCTCAGAGGCAGGAGCCA---ACAGAC------AAGGAACTG---------TATCCTTTAGCTTCCCTCAAATCACTCTTTGGCAGCGACCCA!TAGTCACAATA!!A >Ref.C.IN.95.95IN21068.AF067155 ATGGGTGCGAGAGCGTCAATATTAAGAGGGGGAAAATTAGATAAATGGGAAAAAATTAGGTTAAGGCCAGGGGGAAAGAAACGCTATATGCTAAAACACCTAGTATGGGCAAGCAGGGAGCTGGACAGATTTGCAGTTAACCCTGGCCTTTTAGAGACA---GCAGAAGGCTGTAAACAAATAATAAAACAGCTACAACCA---GCTCTTCAGACAGGAACAGAGGAACTTAGATCATTATTCAACACAGTAGCAACTCTCTATTGTGTACAT---GCAGGGATAGAAGTACGAGACACCAAAGAAGCCTTAGACAAGATAGAAGAAGAA---CAAAACAAAATTAAG---------CAAAAAACACAGCAGGCA------AAAGAGGATGACGGG---------------------------AAGGTCAGTCAAAATTATCCTATAGTGCAGAATCTCCAA---GGGCAAATGGTACACCAAGCCATATCACCTAGAACTTTGAATGCATGGGTAAAAGTAATAGAGGAAAAGGCTTTTAGCCCAGAGGTAATACCCATGTTTACAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAATACCATGTTAAATACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGATACCATCAATGAAGAGGCTGCAGAATGGGATAGATTACATCCAGTACCTGCAGGGCCTATTGCACCAGGCCAACTGAGAGAACCAAGGGGAAGTGATATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGCATGGATGACGAATAAC---------CCACCTGTTCCAGTGGGAGACATCTATAAAAGATGGATAATTCTGGGGTTAAATAAAATAGTAAGAATGTATAGCCCTGTGAGCATTTTGGACATAAGACAAGGGCCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTTTAAAACTTTAAGAGCTGAACAAGCTACACAAGATGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAATCCAGATTGTAAGACCATTTTAAGAGCATTAGGACCAGGGGCTTCATTAGAAGAGATGATGACAGCATGTCAGGGAGTGGGAGGACCTAGCCACAAAGCAAGAGTGTTGGCTGAGGCAATGAGC------CAA---------ACA---------AAC------AGTGCC---------ATACTGATGCAAAGAAGCAATTTTAAAGGCTCTAAAAGAATTGTTAAATGTTTCAACTGTGGCAAGGAAGGGCACCTAGCCAGAAATTGCAGGGCCCCTAGGAAAAAAGGCTGTTGGAAA---TGTGGAAAGGAAGGACACCAAATGAAAGACTGTACTGAAAGGCAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCCACAAGGGGAGGCCAGGGAATTTCCTCCAGAGTAGACCA------------------------------GAGCCAACAGCTCCACCAGCA---------------------------------GAGAGCTTCAGGTTC---GAGGAGACAACC---CCAGCTCCGAAGCAGGAGCCG---AAAGAC------AGGGAA---------------CCTTTAACTTCCCTCAGATCACTCTTTGGCAGCGACCCCTTGTCTCAATAA--- >Ref.B.US.98.1058_11.AY331295 ------------GCGTCAGTATTAAGCGGGGGAAAATTAGATACATGGGAGAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTTGCACTTAACCCTGGCCTGTTAGAAACA---GCAGAAGGCTGTAGACAATTATTGGGACAGCTACAGCCA---TCCCTTCAAACAGGATCAGAAGAACTTAAATCATTATTTAATACAATAGCAACCCTCTATTGTGTACAT---CAAAGGATAGAGGTAAGAGACACCAAAGAGGCTTTAGACAAGATAGAGGAAGAG---CAAAACAAAAGTAAG---------AAAAAAGCACAGCAAGCAGCAGCTGCAGCTGACACAGGAAACAGCAGC------------------CAGGTCAGCCAAAATTACCCTATAGTGCAGAACCTCCAA---GGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAATAGAAGAGAAGGCTTTTAGCCCAGAAGTAATACCCATGTTTGCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAAACCATCAATGAGGAAGCTGCAGAATGGGATAGAATACATCCAGCGCAAGCAGGGCCTATAGCACCAGGCCAGATAAGAGACCCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAACATGGATGACAAATAAT---------CCACCTATCCCAGTAGGAGAAATCTATAAAAAATGGATAATCATGGGATTAAATAAAATAGTAAGGATGTATAGTCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGGGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAACGCGAACCCAGATTGTAAGACTATATTAAAAGCATTAGGACCAGCAGCTACACTAGAGGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCTGGCCATAAAGCAAGAGTTTTGGCTGAAGCAATGAGC------CAAGTA------ACA---------AAT------TCAGGT------GCCATAATGATGCAGAAAGGCAATTTTAGGAACCAG------GTTGTTAGGTGTTTCAATTGTGGCAAAGTAGGGCACATAGCCAAAAATTGCAGGGCCCCTAGGAAGAAGGGCTGTTGGAAA---TGTGGAAAAGAAGGACACCAAATGAAAGATTGTGATCAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCCACAAAGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCA------------------------------GAGCCAACAGCCCCACCAGCA---------------------------------GAGAGCTTCAGGTTTGGGGAGGAGACAACAACTCCCTCTCAGAAGCAGGAGCCA---CAAGAA------------------------TATCCTTTAGCTTCCCTCAGATCACTCTTTGGCAACGACCCCTCGTCACAATAA--- >Ref.J.CD.97.J_97DC_KTB147.EF614151 ------------------------------------------GCATGGGAGAAAATTTGGCTGAGGCGACGGGGAGAGAAAAAATACAGGCGAAAACATATAGTATGGGCAAGCAGGGAGCTGGACAGATATGCACTTAACCCTGGCCTTCTA!!TAGT!GAGCAGAAGGCGGTGAACAGATACTAGTACAGATCCAACCA!GATCTTTA!!AACAGGAGCAGAGGAGATAAAATCATTATTTAACACAGAAGCAACCCTCTATTGTGTACAT!!T!AGAGGATAGACATAAGAGACACCAAGGAGGCTTTAGACAAGATAGAGGAA!CTTTA!!AAACAAAAGCAAG---------GAGAAAGCTAAGAAAGAA------GCTGTCAAAAAATACAACAGT---------------------CAGGTGAGTCACAATTATCCTATATTGCAAAATATG!!T!AAGGGGAACTAGTACACCAGGCCCTATCACCTAGAACATTAAATGCATGGGTAAAGGTGATAGAAGAGAAAGGTTTCAACCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACTCCACAAGATTTAAATACCATGCTAAACACGGTGGGGGGACATCAAGCAGCGATGCAAATGTTAAAAGATACCATCAATGAGGAAGCTGCAGAATGGGACAGGCTCCATCCAGTACATGCAGGACCTGTTGCACCAGGTCAGATGAGAGAACCGAGGGGAAGTGATATAGCAGGAACTACTAGTAACCTTCAGGAACAAATAGCATGGATAACAGGCAACGGTGGCAACCAACCTATCCCAGTAGGAGAAATCTATAAAAGATGGATAATTTTAGGATTAAATAAAATAGTGAGAATGTATAGCCCTGTCAGCATTTTGGACATAAGGCAAGGACCAAAAGAACCTTTTAGAGACTATGTGGATAGGTTCTTTAAAACTCTAAGAGCCGAGCAAGCTACACAGGAGGTAAAAAATTGGATGACAGATACCTTGTTGGTCCAAAATGCGAATCCAGATTGTAAGACCATTCTAAGAGCATTAGGAGCAGGAGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTGAGAGTATCCAGTCATAGAGCAAGAGTTTTTGGTGAGGCAATAAGC------CAAGTA------AAC---------AAT------ACAAAC---------ATAATAATGCAAAGAGGTAACTTTAGGGGCCAGAAGAGAAGTGTTAAATGTTTCAACTGTGGTAAAGAGGGACACATAGCAAAAAATTGCAGGGCCCCTAGAAAAAAGGGCTGT!TGAAA!!GTGTGGAAAGGAAGGACACCAAATAAAAAACTGCACTGAGAGACAGGCCAATTTTTTAGGGAAAGTTTGGCCTTCCAGCAAGGGGAGGCCAGGGAACTTTCTCCAGAGCAGGCCA------------------------------GAACCAACAGCCCCACCAGCA---------------------------------GAAAGCTTCGGGTTCGGGGAGAAGATAACT---CCCTCCCAGAAACAGGAACCG---AGG---------AAGGAACTA---------TATCCTTCAGCTTCCCTCAAATCACTCTTTGGCAGCGACCCCTCGTCACAGTAA--- >Ref.J.CM.04.04CMU11421.GU237072 ATGGGTGCGAGAGCGTCAGTATTAAGCGGCGGAAAATTAGATACTTGGGAGAAAATTCGGTTGAGGCCAGGGGGGAAGAAACGTTATAGGCTAAAACATTTAGTATGGGCAAGCAGGGAGCTGGACAGATTTGCACTTAACCCTGRCCTTCTAGAAACA---TCAAAAGGCTGTCAACAAATATTAGTACAGCTCCAACCA---TCTTATCAAACAGGGACAGAAGAAATTAAGTCATTATATAACACAGTAGCAACCCTCTATTGCGTACAT---GAGGRSATAGAGGTAAAAGACACCAAGGAARCTTTAGACAAGATAGAGGAACTA---CAAAAGAAGAACAAG---------CAACAGGCACAGAAAGCA------GAARCTGACAAAAGRRACARCAGT------------------CAAGTCAGTCAAAATTATCCTATAGTGCAGAACATGCAA---GGGCAACCAGTACAYCARGCCCTATCACCTAGAACTTTAAATGCATGGGTAAAAGTGRTAGAAGARAAGGCTTTYAGCCCAGAAGTAATACCCATGTTTTCAGCYTTATCAGAAGGAGCCACCCCRCAAGATTTAAATACCATGCTAAATACAGTRGGGGGACACCARGCAGCTATGCAAATGTTAAAAGATACTATCAATGAGGAAGCTGCAGAATGGGATAGGKTACATCCAGTACATGCAGGGCCTCCRGCACCAGGCCAGGCGAGAGAACCGAGGGGAAGTGATATAGCAGGAACTACTAGTACCCTCCAGGAACAAATAGCATGGATGACAGGCAAC---------CCACCTATCCCAGTAGGGGAAATTTATAAAAGRTGGATAATTCTGGGATTAAATAAAATAGTRAGAATGTATAGCCCTGTCAGCATTTTGGATATAAGACAAGGACCAAAAGARCCTTTTAGAGAYTATGTAGATCGGTTCTTTAAAACTCTAAGAGCTGAGCAAGCTACACAGGAAGTAAAAAATTGGATGACAGATACCTTGTTGATCCAAAATGCAAATCCAGATTGCAGAACCATYTTAAAAGCATTAGGACCAGGAGCTACACTAGARGAAATGATGACAGCATGYCAGGGAGTGGGAGGACCTGGTCATAAAGCAAGAGTTTTGGCWGAAGCAATGAGC------CAAATG------ACC---------AAT------ACAGCA------AACATAATGATGCAAARGGGTAAYTTTAAGGGCCARAAAAGAATGATTAAGTGTTTCAATTGTGGWAAACCAGGACACCTAGCMAGAAAYTGCAGAGCCCCTAGRAARAAGGGCTGTTGGAAA---TGTGGACAGGAAGGACAYCAAATGAAAGACTGCACTGAGAGACAGGCTAATTTTTTAGGGAARATCTGGCCTTCCAACAARGGGAGGCCAGGGAACTTTCTYCAGAGCAGRCCA------------------------------GAGCCAACAGCCCCACCAGCA---------------------------------GAGAGCTTCGGGTTCGGGGAAGAG---ACC---YCYYCCCCGAAACAAGAAGCG---------------AAGGAACTG---------TATCCTCTAACTTCCCTCAAATCACTCTTTGGCARCGACCCCTYGTCACAATAA--- >Ref.H.GB.00.00GBAC4001.FJ711703 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATGCTTGGGAGAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAGGCTAAAACATCTAGTATGGGCAAGCAGGGAGCTGGACAGATTTGCACTCAACCCCGACCTTTTAGAAACA---GCAGATGGCTGTCTAAAAATAYTAGGACAGATACAGCCA---GCTCTTCAGACAGGAACAGAAGAAATTAAATCGTTATTTAATCTAGTAGCAGTCCTCTATTGTGTACAT---CAGAAAATAGAGGTACAAGATACCAGTGAAGCTTTAAATAAGGTAAAGGAGATA---CAGAACAAGAACCAG---------CAAACAACACAGCAGGCA------ACAGCTRGTAAAGAGAAGGACAGC------------------AAGATCAGTCAAAATTATCCTATAGTACAGAATGCCCAA---GGGCAAATGGTACACCAGGCCATATCACCTAGGACCTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTTAGCCCAGAAGTAATACCCATGTTTTCAGCATTATCAGARGGAGCMACCCCACAAGACYTAAATACCATGTTAAACTCAGTGGGGGGACATCAGGCAGCCATGCAAATRTTAAAAGATACAATCAATGAGGAAGCTGCAGAATGGGATAGGACACATCCAGTGCATGCAGGGCCTATTCCACCAGGCCAGATGAGAGAACCAAGGGGAAGCGATATAGCAGGAACTACTAGYAACCTTCAGGAACAAATAGCATGGATGACARGYAAT---------CCCCCTRTCCCAGTGGGRGAKATCTATAAAAGATGGATAATCWTGGGATTAAATAAAATAGTAAGAATGTATAGTCCTGTCAGCATTTTGGACATAAAACAAGGGCCAAAAGAACCCTTTAGAGAYTATGTAGACAGGTTYTTTAAAACTTTAAGAGCTGAGCAAGCCACACAGGACGTGAAGAATTGGATGACAGACACCTTGTTGGTCCAAAATGCAAATCCAGATTGCAAGACTATTTTAAAAGCATTAGGACAAGGGGCTTCAATAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCTGGCCATAAAGCAAGAGTTTTGGCTGAGGCAATGAGT------CAAATG------ACA---------AAT------ATGAATACA---GCCATAATGGTGCAGAAAGGCAACTTTAAGGGCCAAAGAAGAACTGTTAAATGTTTCAACTGTGGTAAAGAAGGACACATAGCAAGAAACTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAA---TGTGGGAGGGAAGGACATCAGATGAAAGACTGCACAGAGAGACAGGCGAATTTTTTAGGGAAAATCTGGCCTTCCAGCAAAGGGAGGCCAGGGAACTTTCTCCAGAGCAGGCCA------------------------------GAACCAACAGCCCCACCAGCA---------------------------------GAATGCTTCGGGTTCGGGGAGGAGATGACA---CCCCCTCCGAAGCAGGAGATG---AAGGAA------AAGGAA------------CCTCCCTTAACTTCCCTCAGATCACTCTTTGGCAGCGACCCCTTGTCACAGTAA--- >Ref.G.NG.92.92NG083.U88826 GTGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATTCTTGGGAAAAAATTCGGTTAAGGCCAGGGGGAAGGAAAAAGTATAAACTAAAACATATAGTATGGGCAAGCAGGGAACTGGGGAGATTTGCACTTAACCGTGACCTTTTAGAAACA---GCAGAAGGTTGTGTGCAAATAATGAAACAGTTGCAACCA!GCTCTCTA!!GACAGGAACAGAGGAGCTTAGATCATTATTTAATACAGTAGCAACCCTCTACTGTGTACAT---CAAAAGATAGAGGTAAAAGACACCAAAGAAGCTCCAGAGGAAGTGGAAAAAATA---CAAAAGAACAGTCAG---------CAAGAAATACAGCAGGCA------GCAAAGAATGAAGGAAACAGTAAC------------------CCAGTCAGCCAAAATTATCCTATAGTGCAGAATGCACAA---GGGCAAATGATACATCAGGCCATATCACCTAGGACTTTGAATGCGTGGGTAAAAGTAGTAGAAGAAAAGGCCTTCAGTCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAGGGAGCCACCCCACAAGATTTAAATACCATGCTAAATACAGTGGGGGGGCATCAAGCAGCTATGCAAATGCTAAAGGATACTATCAATGATGAAGCTGCAGAGTGGGACAGGATACATCCACAGCAGGCAGGGCCTATTCCACCAGGCCAAATAAGAGAGCCTAGTGGAAGTGATATAGCAGGAACTACTAGTACCCTGCAGGAACAAATAAGATGGATGACCAGCAAC---------CCACCTATCCCAGTGGGAGAAATCTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTGAGAATGTATAGCCCTGTCAGCATTTTGGACATAAGACAAGGGCCAAAAGAACCCTTTAGAGATTATGTAGATAGGTTCTTTAAAACTTTGAGAGCTGAGCAAGCTACACAGGAAGTAAAAGGTTGGATGACAGACACCTTGTTGGTTCAAAATGCGAACCCAGATTGTAAAACCATCTTAAGAGCATTAGGACCAGGAGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCCAGCCATAAAGCAAGAGTTTTAGCTGAGGCAATGAGC------CAGGCA------TCA---------GGT------GCAGCAGCAGCAGCCATAATGATGCAGAAAAGCAATTTTAAGGGCCCGAGAAGAATTATTAAGTGTTTCAACTGTGGCAAGGAAGGACATCTAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAA---TGTGGAAAGGAGGGACATCAAATGAAAGAATGCACGGAAAGGCAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCAACAAGGGGAGGCCAGGAAACTTTCTCCAGAACAGGACA------------------------------GAGCCAACAGCCCCACCAGCA---------------------------------GAGAGCTTCGGATTCGGAGAGGAGATAGCC---CCCTCCCCGAAGCAGGAGCCA---AAGGAG------AAGGAGCTA---------TATCCCTTAACTTCCCTCAAATCACTCTTTGGCAGCGACCCC!TAGTCACAGTA!!A >Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACA---TCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCA---TCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCAT---CAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAG---CAAAACAAAAGTAAG---------AAAAAAGCACAGCAAGCA------GCAGCTGACACAGGACACAGCAAT------------------CAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAG---GGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAAT---------CCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGC------CAAGTA------ACA---------AAT------TCAGCT------ACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAA---TGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCA------------------------------GAGCCAACAGCCCCACCAGAA---------------------------------GAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCG---ATAGAC------AAGGAACTG---------TATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAA--- >Ref.B.TH.90.BK132.AY173951 ATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGACAATTAGATAGATGGGAGAAAATTCGGTTACGGCCAGGGGGAAAGAAAAAATATAGATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTATTGGAAACA---TCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCA---AGCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAATAGCAGTCCTCTATTGTGTACAT---CAAAAGATAGAGGTAAAAGACACCAAGGAAGCTTTAGAGAAGATAGAGGAAGAA---CAAAACAAAAGTAAG---------AAAAAGGCACAGCAAGCA------GCAGCTAACACAGAAAACAGCAGC------------------CAGGTTAGCCAAAATTACCCTATAGTGCAAAATATGCAG---GGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAAAAGGCTTTCAGCCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGATTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACACATAAT---------CCACCTATCCCAGTGGGAGAAATTTACAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGGATGTATAGCCCTACCAGCATTTTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAGACTCTAAGAGCCGAGCAAGCCTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCAGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGTCCCGGCCATAAGGCAAGAGTTTTGGCGGAAGCAATGAGC------CAAGTG------ACA---------AAT------TCAGCT------ACCATAATGATGCAGAAAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACATAGCCCGAAATTGCAGGGCCCCTAGGAAGAAGGGCTGTTGGAGA---TGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAAAGACAGGCTAATTTTTTAGGGAAAATCTGGCCTTCCCACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCA------------------------------GAGCCGACAGCCCCACCAGCA---------------------------------GAGAGCTTCAGGTTTGGGGAAGAGACAACAACTCCCTCTCAGAAGCAGGAGACA---ATAGAC------AAGGAACTA---------TATCCTTTAACTGCCCTCAAATCACTCTTTGGCAACGACCCCTCGTCACAATAA--- bppsuite-2.4.1/Examples/Data/LSU.dnd000066400000000000000000000055221333524216000171350ustar00rootroot00000000000000((((((((Leptospira:0.211857,((((Thermus:0.146936,(Thermotoga:0.107931,Aquifex:0.260721):0.0337762):0.0847738,Synechocystis:0.238263):0.0184171,((((Mycobacterium@smegma:0.0152015,(Mycobacterium:0.00677954,Mycobacterium@leprae:0.0189232):0.0143038):0.0519384,Rhodococcus@erythrop:0.0241529):0.0377471,(Frankia@sp:0.0326741,(((Thermomonospora:0.0376728,Microbispora:0.0431383):0.0171155,Thermomonospora@chro:0.0276944):0.0409298,((Streptomyces@coelico:0.012891,Streptomyces@griseus:0.0125734):0.00768632,Streptomyces@rimosus:0.0118849):0.0466048):0.00997886):0.0239115):0.000373145,((Micrococcus:0.0609534,Renibacterium:0.0251235):0.0215017,Tropheryma:0.0967747):0.0168714):0.121323):0.0211992,((((((((Bacillus@licheniform:0.00347702,Bacillus@stearotherm:0.0611505):0.0157103,Listeria@monocytogen:0.0389548):0.00972441,Bacillus@globisporus:0.0338981):0.0139857,Staphylococcus@pisci:0.0512119):0.0131618,(Enterococcus:0.0156791,((Lactobacillus:0.0711563,Leuconostoc@lactis:0.0664503):0.0255861,(Lactococcus:0.0633394,Streptococcus:0.026513):0.0378023):0.0136943):0.0239073):0.0392089,Erysipelothrix@rhusi:0.116809):0.0189999,Peptococcus:0.162782):0.0129891,Clostridium@botulinu:0.146896):0.0409783):0.0148788):0.0190659,((((((((Burkholderia@mallei:0.0155984,Ralstonia@solanacear:0.0236959):0.0181518,(Alcaligenes:0.0398318,Bordetella@bronchise:0.0255562):0.021133):0.0286949,Neisseria@meningitid:0.0681373):0.0483249,((Leucothrix:0.0878135,Xylella:0.0788572):0.00758399,((((Ruminobacter:0.124861,Aeromonas@hydrophila:0.0264272):0.0176731,(Vibrio@cholerae:0.0463728,((((Escherichia@coli:0.0041224,(Klebsiella:0.00405158,Citrobacter:0.00636193):0.00398771):0.00390397,Salmonella@bongori:0.0128143):0.0142482,Buchnera@aphidicola:0.073711):0.0146922,Haemophilus:0.0712366):0.0215992):0.00983827):0.0423124,Acinetobacter:0.077717):0.0167588,Pseudomonas@stutzeri:0.046158):0.0192256):0.0131933):0.0129048,Thiobacillus:0.0996059):0.0467108,(((Rickettsia:0.122587,(((Rhodopseudomonas@pal:0.0117125,Bradyrhizobium:0.0178525):0.0746991,((Zoogloea:0.018863,Agrobacterium@vitis:0.0192032):0.0222354,(Brucella:0.0169999,Bartonella:0.0275871):0.0176813):0.0257604):0.0160184,Brevundimonas:0.112224):0.00968614):0.00878232,(Rhodospirillum:0.0582425,((Paracoccus:0.0252502,Rhodobacter:0.0348436):0.0105068,Rhodobacter@sphaeroi:0.0259512):0.0760798):0.0177725):0.0169304,Zymomonas:0.125582):0.068287):0.043152,(Stigmatella:0.150748,Nannocystis:0.146526):0.0377841):0.0317373,((Helicobacter@pilori:0.0638338,Wolinella:0.0304204):0.0561446,Campylobacter@jejuni:0.0864261):0.128797):0.0266729):0.00685327,(Treponema:0.167452,Borrelia:0.108701):0.116383):0.0207078,(Mycoplasma@hyopneumo:0.216042,Ureaplasma:0.234444):0.0737392):0.0230123,Pirellula:0.258376):0.149483,Waddlia:0.047224):0.00888048,(Chlamydia@sp:0.0362833,Simkania:0.0716742):0.0186897):0.0722677,Chlamydophila@felis:0.0255132,Chlamydia@muridarum:0.0182393); bppsuite-2.4.1/Examples/Data/LSU.phy000066400000000000000000007003161333524216000171730ustar00rootroot0000000000000079 2353 Bradyrhizobium TGCTTAAGGTGTTCGGTGGATGCCTTGGCGCTGAGGCGATGAAGGACGTGCTACCTGCGATAAGCCGTGGGGAGCTGCGAAAAGCTTGATCCATGGATTT CCGAATGGAGACATCAGCAACCCAGGGACTGAAACATCTAAGTACCTGGGGAAAGGACATCAACGAGACTCCGTTAGTAGTGGCGAGCGAACGCGGACCA GGCCATAACAATCGGAACCGGTAGGAAACCGGGCCCAGAGGTGAAGCCCCGTAGAAATCCAGAGTAGGCGGGACACGTGAAATCCTGTCTGAACGCGGGG GGACCACCCTCCAAGCCTAAGTACTCTCAGCGACCGATAGTGAACAGTACCGTGAGGAAAGGTGAAAAGCCCGGAGTGAAAAGACTGAAACCGGACACCT ACAACAGATGGAGCCCCGGGTGACATGTACCTTTTGTATTATGGGCCAGCGACTTAATTTAACGAGCAGCTTAAGATGGTAGGCGCACGGAGCGGTCTGA ATAGGGCGAAGTTCGTTGTATTAGACCCAAACCAGTGATCTAGCCATGAGCAGTTGAAGGTGAGTAACACTCACTGGAGGACCGAAGGTGCCTGTTGAAA AAGGCCCGATGACTGTGTTAGGGGTGAAAGGCCAATCAAACTGGAAATAGCTGGTCTCCGCGAAAGATATTTAGGTAGCGCCTCGGATACCTCAGGGGTA GAGCACTGGATGGGCTAGGGATCTCTAAACCCAACCAAACTCCGAATACCTGTATCCGGGAGTCACACGCGGGTGCTAACGTCCGTCGTGGAGAGGGAAA CAACCCGGACCTACAGCTAAGCCCCTAATCTGGCTAAGTGGAAAGGATGTGAAATCCCAAAACAACCAGGAGGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAACAGCTCACTGGTCTAGGGTTTCCCGAAGATGTCGGCTAAGCCACGAGCCGAAGCTTAGGGTCAGCGGTAGCGGAGCGTTCTGTACCTGCAAGGGG ACTCGTGAAGCGCCTGGAGGTATCAGAAGTGCGAATGTGGCATGAGTAACGAAACACTGTGAAAGACAGTGTCGCCGAAAGTCCAAGGTTCCTGCGTAAG TTAATCTTCGCAGGGTTAGCCGGTCCCTAAGGCGAGGCCGAACGTAGTCGATGGGAATGCAGGAATATTTGCAGCGTGACGAATCCCGTGGTTGTCGACA CTGGTTGCTTCGGTTCCAGGAAATACACCGTACCAAACCGACACAGGTGGACGGTAGAGTATACCAAGGCGTTGAGAGAACTATGTTGAAGGAACTCGGC AATTTACCTCCGTAACTTCGGGATAAGGAGGCCCATCAATGGGGCACAGACCGGGGGGGAACTGTTTAACAAAAACACAGGCTCTGCGAAATCGCAAGAT ACGTATAGGGTCTGACGCCTGCCCGGTGCCGGAAGGTTAAGAGGAGAGGTCAAGCTTGAATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAATGACTTCCCCGCTGTCTCCAACATAGACTCAGTGAAATTGAATTCCC CGTGAAGATCGGGGTTCCTGCGGTCAGACGGAAGACCCCGGCACCTTTACTGTAGCTTTGCGCTGGTATTCGTGACTGTTTGTGTAGAATAGGTGGTAGG CTTTGAAGCCGTGGCGCCAGCCATGGTGGAGCCAAATGAAATACCACCCTAATGGTTATGATATCTAACCGCGAGACCGGGACAGCGCATGGTGGGCAGT TTGACTGGGGCGGTCGCCTCCCAAAGAGTAACGGAGGCGTGCGAAGGTAGGCTCAGAACGGTCGGAAATCGTTCGTCGAGTATAATGGCATAAGCCTGCC TGACTGCGAGATCTACGATGAGCAGAGACGAAAGGGTCATAGTGATCCGGTGGTCCCGGTGGATGGGCCATCGCTCAACGGATAAAGGTACGCCGGGATA ACAGGCTGATGACGCCCAAGAGTCCATATCGACGGCGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGGAGAAGGTCCAAGGGTTCGCTG TTCGCCGATAAAGTGGTACGTGAGCTGGGTTCAGAACGTGTGAGACAGTTCGGTCCCTATCTGCCGTGGGTGTTGGAATTTGAGAGGATTGCCCCTAGTA CGAGAGGACCGGGGTGAACGTACTCTGGTGGAGCTGTTGTCGCGCCAGCGCATGCAGCATAGCTATGTCGGCGGGATAACCGCTGAAACATCTAAGCGGA AACCCCCTAAAAGAGCATTCCCAGAACCGTGGAAGACCACACGTGATGGCCGG Bacillus@licheniform TTAGAAAGGCGCACGGTGGATGCCTTGGCACTAAGCCGATGAAGGACGGGACGACACCGATATGCTTCGGGGAGCTGTAAGAAGCTTGATCCGGAGATTT CCGAATGTCCTCATGAGCAACCCGGGGACTGAAACATCTAAGTACCCGGGGAAGAGAAAGCAAAGCGATTCCCTGAGTAGCGGCGAGCAAAACGGGAACA GCCCGGAGGTAGATGAAGGGTCTGGAAAGCCCGCCTAGGGGTAAAGCCCTGTATCAACCCTGAGTCGGCGGAACACGTGAAATTCCGTCGGAATCCGGGA GGACCATCTCCCAAGGCTAAATACTCCTAGTGACCGATAGTGAACAGTACCGTGAGGAAAGGTGAAAAGCCCGGAGTGAAAAGTCTGAAACCGTGTGCCT ACAATAGTCAGAGCCCAGGGTGATGGGTGCCTTTTGTAGAATGAACCGGCGAGTTACGATCCCGTGCAGGTTAAGAAAGGAGCCGCAGCGAGCGGTCTGA ATAGGGCGGAGTACGTGGTCGTAGACCCAAACCGGTGATCTACCCATGTCCAGGTGAAGTTCAGTAACACTGAATGGAGGCCCGAACACGCACGTTGAAA AGTGCGGGATGAGTGTGGTAGGGGTGAAATGCCAATCGAACCTGAGATAGCTGGTCTCTCCGAAATAGCTTTAGGGCTAGCCTCAAGAGATCTTGAGGTA GAGCACTGATTGGACTAGGCCTCGGTAAATTCAGTCAAACTCCGAATGCCAATACTTGGGAGTCAGACGCGAGTGATAAGATCCGTAGTCGAAAGGGAAA CAGCCCAGACCGCCAGCTAAGTCCCAAAGAACGTTAAGTGGAAAGGATGTGAGTTGCTTAGACAACCAGGATGTTGCTTAGAAGCAGCCTTTAAAGAGTG CGTAATAGCTCACTGGTCGAGTGACTCCCGAAAATGTCGGCTAAACGTATCACCGAAGCTGCGGACTGGTGGTAGGAGAGCGTTCTAAGGCTGTAAGCGA GACCGGAAGACTCGTGGAGCGCTTAGAAGTGAGAATGCGGTATGAGTAGCGAAGAGGGGTGAGAATCCCCTCCACCGAATGCCTAAGGTTCCTGAGGAAG CTCGTCCGCTCAGGGTTAGTCGGGACCTAAGCCGAGGCCGAACGTAGGCGATGGACAACAGGTGATATTCTGTACGGGACGCAGAGGATAGGGTACGCGT TGGCGCGTCCTCCTGCCAAGAAAAGCCCCGTACCAAACCGACACAGGTAGGCAGGAGAGAATCCTAAGGTGTCGAGAGAACTCTCGTTAAGGAACTCGGC AAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCTCAGGGCCGCAGTGAATGGCCCAGGACTGTTTAGCAAAAACACAGGCTCTGCGAAGCCGTAAGGC AAGTATAGGGGCTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGAGCGCTTAAGTGCGAATTGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCCGCACGAAAGGCGCAACGATCTGGGCACTGTCTCAACGAGAGACTCGGTGAAATTATAGTACC TGTGAAGATCAGGTTACCCGCGACAGGACGGAAGACCCCGGGAGCTTTACTGCAGCCTGATATTGAATGTTGGTACAGCTTGTACAGGATAGGTAGGAGC CTTGGAAACCGGAGCGCCAGCTTCGGTGGAGGCTCGTGGGATACTACCCTGGCTGTATTGCCTTCTAACCCGCATAGGGAGACAGTGTCAGGTGGGCAGT TTGACTGGGGCGGTCGCCTCCTAAAAGGTAACGGAGGCGCCCAAAGGTTCCCTCAGAATGGTTGGAAATCATTCGCAGAGTGTAAAGGCACAAGGGAGCT TGACTGCGAGACCTACAGTGAGCAGGGACGAAAGGGGCTTAGTGATCCGGTGGTTCCGATGGAAGGGCCATCGCTCAACGGATAAAGCTACCCCGGGATA ACAGGCTTATCTCCCCCAAGAGTCCACATCGACGGGGAGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGGGCTGTAGTCGGTCCAAGGGTTGGCTG TTCGCCCATAAAGCGGTACGCGAGCTGGGTTCAGAACGTGTGAGACAGTTCGGTCCCTATCCGTCGCGGGCGCAGGAAATTGAGAGGACTGTCCTTAGTA CGAGAGGACCGGGATGGACGCACGCTGGTGTACCAGTTGTTCTGCCAAGGCACGCTGGGTAGCTATGTCGGCGGGATAAGTGCTGAAACATCTAAGCATA AGCCCCCTAAGAGAGATTTCCCAGATCCCTGAAAGATGATAGGTGATGGTCTG Rickettsia TAAATAAGGCATTTGGTGGATGCCTTGGCACTAAGGCGATGAAGGACGTGATACCTGCGATAAGCTTCGGGGAGTTGCGAAAAACTTGATCCGAAGATTT CCGAATATTGACATGAGCAACCCAGCGACTGAAATATCTAAGTAGCTGGGGAAAGGACATCAACGAGACTCCGTTAGTAGTGACGAGCGAACGCGGATCA GGCCGCTATAACTAAAACAACATGGAAAGTTGACCTAGAGGTGAAGTCCCGTAAGAAACCTGAGTAGGCGGGACACGTGAAATCCTGTTTGAACATAGGG GGACCACCCTCTAAGCCTAAGTACTCCTAGTGACCGATAGTGAAAAGTACCGTGAGGAAAGGTGAAAAGTCCGGAGTGAAAAGACTGAAACCAAATGCTT ACAACAGTCGGAGCAAATTGTGACGGGTACCTTTTGTATAATGGGTCAGCGACTTAGTTTATCTAGCAGCTTAAGTTGGTAGGCGTAGCGAGCGGTCTGA ATAGGGCGTAGTTAGATGAATTAGACCCAAACCGGTGATCTAGCCATGGCCAGTTGAAAGCGGATAAAATCCACTGAAGGACCGAACACTACTGTTGAAA AAGTAGGGATGAGTGTGTTAGGGGTGAAAGGCCAATCAAACTCGATATAGCTGGTCTCCGCGAAATCTATTTAGGTAGAGCGTTATATACCATCGAGGTA GAGCACTGAATGAGCTAGGGTCCACTAAACTCAATCAAACTCCGAATGTCGGTACATAGCAGACAGACATGGGTGCTAAGGTCCATAGTCGAGAGGGAAA AAGCCCAGATCGCCATCTAAGTCCCTAAACTGACTAAGTGTAAAGGATGTAGAAGACCAAAACAACTAGGATGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAATAGCTCACTAGTCTAGTTTTCTCCAACAATGTCGGCTAAGTCATGTACCGAAGATGCGGGTTTATGGTAGCGGAGCGTTCCGTACCTGCAAGGTG AACCGTAAGTTTGCTGGAGGTATCGGAAGTGAGAATGTGACATAAGTAGCGAAAGAATGTGAGAAACATTCTCGCCGAAAGTCCAAGGTTCTTGCGTAAG TTAATCTGCGCAAGGTTAGTCGGCCCCTAAGATGAGGCTGAACGTAATCGATGGGAATCAGGTAATATTCTGAACGTGACGAAAATAGTAATTGTCAGTA TTGATTGCGGTTTTTCCAGGAAATACACCGTACCAAACCGACACAGGTGGACGGTAGAGTATACCAAGGCGTTGAGAGAACGATGCTGAAGGAACTAGGC AAATTGCATCTGTAACTTCGGAAGAAAGATGACCTGCAGAGTGGCACAAGCTGGGGGAGGACTGTTTATTAAAAACACAGGCTCTGCAAAGTCAATAGAC ATGTATAGGGTCTGACGCCTGCCCAGTGCTGGAAGATTAAAAGGAGGGGTCAAGTCTGAATTGAAGTCCCAGTGAACGGCGGCCGTAACTATGACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCCGCACGAATGGCGTAACGATTTCCCCACTGTCTCCAGTATCGACTCAGCGAAATTGAATTCTC CGTGAAGATCGGAGTTCCCGCGGTCAGACGGAAGACCCCGGAACCTTTACTATAGCTTTGCACTGGTGTTAGGAATCAGATGTGCAGGATAGGTGGGAGA CTACGAAGCGAAGGCGTCAGCCTTTGTGGAGTCCCCTGAGATACCACCCTTTTGGTGCTTACATCTAACCGAGATTCCGAGACAATGCATGGTGGGTAGT TTGACTGGGGCGGTCGCCTCCCAAAGAGTAACGGAGGCGCGCGATGGTTAGCTCAGGTTGGTCGGAAATCAACTTTAGAGTGCAATGGCATAAGCTAGCC TGACTGCGAGTCTGACAGAGAGCAGAGACGAAAGGGTCATAGTGATCCGGTGGTTCCGGTGGAAGGGCCATCGCTCAACGAATAAAGGTACTCCGGGATA ACAGGCTGATGATTTCCAAGCGTCCATAGCGACGAAATGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGGAGAAGGTCCAAGGGTTCGCTG TTCGCCGATAAAGTGGTACGTGAGCTGGGTTTAGAACGTGTGAGACAGTTCGGTCCCTATCTGCCGTGGGTGTAGGAAGTTGAGAGGACTGCCTTTAGTA CGAGAGGACCGAGGTGGACGTACCCTGGTGGACCAGTTGTCGTGCCAACGCAAGCTGGGTAGCTAAGTCGGAGGGATAACTGCTGAATCATCTAAGCAGA AACCCCCTAAAATAGACTTCCCAGAGCCGTGGAAGACCACACGTGATGGTCGG Lactobacillus TAGAAAAGGCGCACGGTGAATGCCTAGGCACTAAGCCGATGAAGGACGTAACGACTGCGAAAAGCTTCGGGGAGCTGTAAGAAGCTAGATCCGGAGATGT CCGAATGTTGGTTAAAGAAACGCAGCGACTGAAACATCTAAGTAGCTGCGGAAGAGAAAGAAAATCGATTTCCTTAGTAGCGGCGAGCGAAGAGGAAAGA GCCTGGAGATAGCAGAACTACCTGGGAAGTAGGCCGAGAGGTGAAGCCCCGTAGCAATCCTGAGTGGGCGGAACACGAGGAATTCCGTTTGAATCCGCGA GGACCATCTCGCAAGGCTAAATACTACTAGTGACCGATAGTGAACAGTACCGTGAGGAAAGGTGAAAAGACCGGAGTGAAAAGACTGAAACCGTGTGCCT ACAATAGTCAGAGCACAGTGTAATGGGTGCCTTTTGTAGAATGAACCGGCGAGTTATGCTGTGCAGCGGGTTAAGAAAGGAGCCGGAGCGAGCGGTCTGA AGAGGGCGAAGTTGTGCGGTGTAGACCCAAACCAGTGACCTACCCATGACCAGTTGAAGGTGCGTAAAACGCACTGGAGGACCGAACACGTAAGTTAAAA ATTGCGGGATGAGTGTGGTAGCGGTGAAATTCCAAACGAACTTGAGATAGCTGGTCTCTCCGAAATAGCTTTAGGGCTAGCCTCGTGAGGTAATGAGGTA GAGCTCTGTTTGGACAAGGCCGCGGTAAATCCAGATAAACTGCGAATTCCAGCACACGGGAGTCAGACGCGAGTGATAAGATCCGTAGTCGAAAGGGAAA CAGCCCAGATCACCAGTTAAGTCCCCAAACATGCTAAGTGGAAAGGATGTGAGTTGCGTAGACAACTAGGACGTTGCTCAGAAGCAGCCTTCAAAGAGTG CGTAATAGCTCACTAGTCGAGTGGCTCCCGAAAATTTCGGCTAAGCATAGTACCGAAACTGTGGACAAGTGGTAGGAGAGCGTTCTAAGGCGGAAAGTCT GATCGAGAGACAGATGGAGCGCTTAGAAGTGAGAATGCGGTATGAGTAGCGAAGATAGGTAAGAATCCTATCCGCCGGAAGACTAAGGTTCCTGGGGCAG CTCGTCCGCCCAGGGTAAGTCGGGACCTAAGGCAAGGCCGAACGTAACCGATGGATAACAGGAGAGATTCTGTACGGGACGCAGAGGCGAAGCACCATGC TGGCATGTGCACCTGCCAAGAAAAGCCCCGTACCAAACCGACACAGGTAGTCAGTGGAGAACACTAAGGTGGCGAGAGAACTCTCGTTAAGGAACTCGGC AAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTGAAGACGCCGCAGAGAATGGCCCAAAACTGTTTATCAAAAACACAGGCTCTGCAAAGTCGTAAGAC ACGTATAGGGGCTGACACCTGCCCGGTGCTGGAAGGTTAAGAGGAGTGCTTCGGTACGAATTTAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAAAGGTGTAATGATTTGGGCACTGTCTCAACGAGAGACTCGGTGAAATTATAATACC CGTGAAGATCGGGTTACCCGCGACAGGACGGAAGACCCCAGGAGCTTCACTGTAGCTTGATATTGAGTATCTGTTAAACATGTACAGGATAGGTAGGAGC CAGAGAAGGTAGGACGCTAGTCTTACTGGAGGCATGTGGGATACTACCCTTGTTTGATGGTGCTCTAACCTAGAGCAGGGGACAGTGTCAGGTAGGCAGT TTGACTGGGGCGGTCGCCTCCTAAAGTGTAACGGAGGCGCTCAAAGGTTCCCTCAGAATGGTTGGAAATCATTCGCAGAGTGTAAAGGTATAAGGGAGCT TGACTGCGAGAGAGACACTGAGCAGGGACGAAAGGGACTTAGTGATCTGGTGGTACCGATGGAAGGGCCATCACTCAACGGATAAAGCTACCCTGGGATA ACAGGCTTATCTCCCCCAAGAGTTCACATCGACGGGGAGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGAAGTTGGTCCAAGGGTTGGATG TTCGCCCATAAAGCGGCACGCGAGCTGGGTTCAGAACGTGTGAGACAGTTCGGTCCCTATCCGTCGTGGGCGCAGGAAATTGAGAGGACTGTCCTTAGTA CGAGAGGACCGGGATGGACGCACGCTGGTGTACCAGTTGTCTTGCCAAAGCACGCTGGGTAGCTATGTCGGAGGGATAAGCGCTGAAACATCTAAGTGCA AGCCCCCTAAGAGAGATTTCCAAGACACCTCAGAGACGATAGGTGATGGCTGG Aquifex TTAGTAAGGCCCGGGGTGGATGCCTCGGCTCCCAGCCGATGAAGGGCGTGCAAACTGCGATAAGCCGGGTGGAGGCGCAAGAGCCGTGAGGCCCGGATGC CCGAATGTCCTTCGGAGGGACCGGCCGAGCAAAACCTTTTAGTAGGCCGGGAAAGGAAATCAATGAGACGCCCTGAGTAGCGGCGAGCGAAAGGGGCTCA GCCCGGACCTAGCCGAAGTCCCTGGAATGGGCGCCTAGAGGTGAAGCCCCGTAGCAAGCCCAAGTCCGCGGCCCACGTGAAAGGTCGCGGGAATCCGGGG GGACCACCCTCCAAGGCTAAGTACTCCGGGAGACCGATAGCGCATAGTACCGTGAGGAAAGGTGAAAAGACCTGAGTGAAAAGACTGAAACCCCGGGTCC ACAACAGTGGAAGGGGTCCCCGACTGGTGCCTTTTGCAGAATGAGCCGGGGAGTTGTCCTCAGGGGCGGGCTAAGTCGGAAGCCGTAGCGAGCGGTCCGA ATAGGGCGAAGTCCCTGGGGGCAGACGCAAGCCGGCGATCTACCCTTGCCCTGGTGAAGGCCGGTAACACCGGCTGGAGGCCCTAAGGTCGGTGCTGCAA AACCGCCCGTGAGTGAGGTAGCGGTGAAAAGCCAATCGCGCCCGGGATAGCTCGTCTCCCCGAAATGCATCGAAGTGCAGCGTCGCCCCTTCCCGAGGTA GAGCACTGCTGGGGCTAGCCCGAGGGAAACCCCGGCAAACTCCGAATGCCGGAGGGCGGCAGTGAGTCTCGGGGGATAAGCTCCGAGGACAAGAGGGAAA CAGCCCAGACCGCCGGCTAAGCCCCAAAGCGGGCTAAGTGGAAAGGAAGTCCCGTCCTAAGACAGCCGGGAGGTTGCTTAGAGGCAGCCTTTAAACAGTG CGTAACAGCTGACCGGTCGAGGGCGGGCCGAAAATTTCGGCTAAGCCCGGCGCCGAAGCCGCGGGTCCGCGGTAGGGGAGCGTTCCCAGGCGCTAAGCCA AGCCGTGAGCAGGGTGGAGCGCTGGGAAGTGAGAATCCGGCATGAGTAGGAGAGGCAGGTGAGAAACCTGCCCGCCGGAAGCCCAAGGTTCGGCGGCAAG GAAATCAGCCGCCGGTTAGCCGGGCCCTAAGGCGAGGCCGAGCGTAGCCGATGGGAAGCGGGCAACATTCCGCGCGTGACGCAGAGGCTAGGCCGGCCCA TGGGGGTGGCCCCTGCCAAGAAACACCCCGTACCAAACCGACACAGGTGGGCGGGTTAGGAGCCTAAGGCGTCGGGGGAACTCCCCTCAAGGAACTCGGC AAGTTGGCCCCGTACCTTCGGAAGAAGGGGTGCCCGCGGGGTCGCAGTGACAGGCGGGCGACTGTTTACCAAAAACACAGGCTACGCAAACCCGAAAGGG ATGTATGTGGTCTGAAGCCTGGCCAGTGCCCGAAGGTGAAGGCCCCCGGTATGGTGGGGGCTGAAGCCCGGGTAAACGCCGGCCGTAACTATGACGGTCC TAAGGTAGCGAAATTCCTTGCCGGGTAAGTTCCGGCCTGCATGAATGGCCCAACGAGTGCCGCACTGTCTCGAGGGGAGTCCCGCCGAAATTGTAATGCC GGTCAAGATCCGGCTACCCGCGGCAGGACGGAAGACCCCGGAAGCTTCACTGCAGCCTGGCATTGGGCTCTGGCCTGTCCTGCGCAGGATAGGTGGGAGC CTGGGAAGCCCCCGCTCCGGCGGGGGTGGAGGCCCGTGAGATACCACCCTGGACAGGCTGGGTCCTAACCCAGATGCGGGGACAGTGCTAGGTGGGCAGT TTAGCTGGGGCGGCTGCCTCCTAAAGAGTAACGGAGGCGCCCAAAGGTCCCCTCAGGCGGGTCGGAAATCCGCCGTAGAGTGCAAGGGCATAAGGGGGCC TGACTGTGAGGCCGACGGCGAGCAGCCGCGAAAGGGGCCTAGTGACCCACCCGCTCCAGTGGGAGGGCGGGTGATCAGCGGATAAAGCTACTCCGGGATA ACAGGCTAATCGCCCCCGAGAGCCCACATCGACGGGGCGTTTGGTACCTCGATGTCGGCTCCCCCCATCCTGGGGCTGAAGCAGGTCCAAGGGTTGGCTG TTCGCCCATAAAGGGGGACGCGAGCTGGGTTCAGAACGTGCGAGACAGTTCGGTCCCTATCCGCCGCGGGCGCAGGAGCTTGAGGGGGCCGTCCCTAGTA CGAGAGGACCGGGACGGGGCAGGACTGGTGTACCGGTTGTCCCTGGAGGGCACGCCGGGTAGCCATCCGCTCGGGATAAGCGCTGAAACATCTAAGCGCA AGCCCCCCAAGAAAGGGCTCCCAGGGCCCCGGGAGACTACGGGTGATGGCCGC Haemophilus TGACTAAGGTACAAGGTGGATGCCTTGGCAATCAGGCGAAGAAGGACGTGCTAACTGCGAAAAGCTTGGATGAGTCGATAAAGGCTTTAATCCAAGATAT CCGAATGTCATCATGAGCAACCGGGAGACTGAAACATCTAAGTACCCCGGGAAAAGAAATCAACGAGATTTCGTCAGTAGCGGCGAGCGAAAGCGAAAGA GCCAAAGGTGAGGAGAATGTGTTGGGAACACAATCAAGAGGTGAAATCCCGTACTAAACGAAAGTGGGCGGGACACGTGATATCCTGTTTGAAGAAGGGG GGCCCATCCTCCAAGGCTAAATACTCTGATTGACCGATAGTGAACAGTACTGTGAAGAAAGGCGAAAAGACCGGAGTGAAAAGACTGAAACCTTGTACGT ACAACAGTGGGAGCGAATTGTGACTGGTACCTTTTGTATAATGGGTCAGCGACTTATATTTTGTAGCGGGTTAACAAGGGAGCCGAAGGGACCGGTCTTA ACTGGGCGTAGTTGCAAGGTATAGACCCAAACCGGTGATCTAGCCATGGGCAGTTGAAGGTTGGTAACACTAACTGGAGGACCGAAGACTAATGTTGAAA AATTACGGATGACTGTGCTGGGGGTGAAAGGCCAATCAAACCGGAGATAGCTGGTCTCCCCGAAATCTATTTAGGTAGAGCCTTGAGCACCTTTGGGGTA GAGCACTGTTTCGGCTAGGGCTCGCTAACCCGATGCAAACTACGAATACCAATGCTCAGGAGACACACGCGGGTGCTAACGTCCGTCGTGGAGAGGGAAA CAACCCAGACCGCCAGCTAAGTCCCCAAGCATATTAAGTGGAAACGAAGTGGAAGGCTTAGACAGCTAGGATGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAATAGCTCACTAGTCGAGTCGGCCCGGAAGATGTCGGCTAAATATAGCACCGAAGCTGCGGCATTTGGGTAGGGGAGCGTTGTGTACGGAAAAGGTT CATCGAGAGTGGGCTGGACGTATCACAAGTGCGAATGTGACATAAGTAACGAAAACGGGTGAAAAACCCGTTCGCCGGAAGACCAAGGTTCCTGTCCAAG TTAATCGGGGCAGGGTGAGTCGGCTCCTAAGGCGAGGCTGAACGTAGTCGATGGGAAACAGGTAATATTCTGTACGGGACGGAGAGGTTAGGTTACGCAT TGGTGCGAACTCCTTCCAGGAAAAGCACCGTACTAAACCGACACAGGTGGTCGGTAGAGAATACTCAGGCGTTGAGAGAACTCGGGTGAAGGAACTAGGC AAAATAGCACCGTAACTTCGGGAGAAGGTGCGCCGGTAACGTCGAAGATACCGCTGGTGAACTGTTTATTAAAAACACAGCCTCTGCAAACACGAAAGTG ACGTATAGGGTGTGATGCCTGCCCGGTGCTGGAAGGTTAATTGATGGTGTAAAGACCTGATCGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCATAATGATGGCCAGGCTGTCTCCACCCGAGACTCAGTGAAATTGAAATCGC CGTGAAGATCGGTGTACCCGCGGCTAGACGGAAGACCCCGGAACCTTTACTATAGCTTGACACTGAACATTGAATTTTGATGTGTAGGATAGGTGGGAGC CTTTGAAGCAGTGACGCCAGTCATTGTGGAGGCACCTGAAATACCACCCTTTAACGTTTGTGTTCTAACGAAGAATCTCGGACAGTGTCTGGTGGGTAGT TTGACTGGGGCGGTCTCCTCCCAAAGCGTAACGGAGGAGCACGAAGGTTTGCTAATCACGGTCGGACATCGTGAGGTTAGTGCAATGGTATAAGCAAGCT TAACTGCGAGACAGACAGTGAGCAGGTACGAAAGGGTCATAGTGATCCGGTGGTTCTGATGGAAGGGCCATCGCTCAACGGATAAAGGTACTCCGGGATA ACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGAAGTAGGTCCAAGGGTATGCTG TTCGCCATTAAAGTGGTACGCGAGCTGGGTTTAGAACGTGTGAGACAGTTCGGTCCCTATCTGCCGTGGGCGTAGGATGTTGATTGGGCTGCTCCTAGTA CGAGAGGACCGGAGTGGACGCATACTGGTGTTCCGGTTGTGTCGCCAGACCATGCCGGGTAGCTAAATCGGAGAGATAAGTGCTGAAACATCTAAGCACA AACTTCCAGAGAGAGTCATCCCAGGGTTGTTGTAGACTACACGTGATGGTTGG Escherichia@coli CGACTAAGGTACACGGTGGATGCCCTGGCAGTCAGGCGATGAAGGACGTGCTAACTGCGATAAGCGTCGGTAAGGTGATATAACCTTTAACCGGCGATTT CCGAATGTCACCATGAGCGACCGGGGGACTGAAACATCTAAGTACCCCGGGAAAAGAAATCAACGAGATTCCCCCAGTAGCGGCGAGCGAACGGGGAGCA GCCCAGCGTTAGTGGAAGCGTCTGGAAAGCGCGCGTACAGGTGAAGCCCCGTAACAAAGATGAGTGGGCGGGACACGTGGTATCCTGTCTGAATATGGGG GGACCATCCTCCAAGGCTAAATACTCTGACTGACCGATAGTGAACAGTACCGTGAGGAAAGGCGAAAAGACCGGAGTGAAAAGACTGAAACCGTGTACGT ACAACAGTGGGAGCACAGTGTGACTGGTACCTTTTGTATAATGGGTCAGCGACTTATATTCTGTAGCAGGTTAACAAGGGAGCCGAAGGGACCGGTCTTA ACTGGGCGAAGTTGCAGGGTATAGACCCAAACCGGTGATCTAGCCATGGGCAGTTGAAGGTTGGTAACACTAACTGGAGGACCGAAGACTAATGTTGAAA AATTACGGATGACTGTGCTGGGGGTGAAAGGCCAATCAAACCGGAGATAGCTGGTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGCATCTCCGGGGTA GAGCACTGTTTCGGCAAGGGTTCACTAACCCGATGCAAACTGCGAATACCGGTGCACGGGAGACACACGCGGGTGCTAACGTCCGTCGTGAAGAGGGAAA CAACCCAGACCGCCAGCTAAGTCCCAAAGCTGGTTAAGTGGAAACGATGTGGAAGGCCCAGACAGCCAGGATGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAATAGCTCACTGGTCGAGTCGGCCCGGAAGATGTCGGCTAAACCATGCACCGAAGCTGCGGCATATGGGTAGGGGAGCGTTCTGTACCTGCAAGGTG TGCTGTGAGCATGCTGGAGGTATCAGAAGTGCGAATGTGACATAAGTAACGAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGTTCCTGTCCAAG TTAATCGGGGCAGGGTGAGTCGACCCCTAAGGCGAGGCCGAACGTAGTCGATGGGAAACAGGTAATATTCTGTACGGGACGGAGAGGCTATGTTGCCGGA CGGCCGGAACACCTTCCAGGAAAAGCATCGTACCAAACCGACACAGGTGGTCGGTAGAGAATACCAAGGCGTTGAGAGAACTCGGGTGAAGGAACTAGGC AAAATGGTGCCGTAACTTCGGGAGAAGGCACGCTGATTACGTCGAAGATACCGCTGGTGAACTGTTTATTAAAAACACAGCCTGTGCAAACACGAAAGTG ACGTATACGGTGTGACGCCTGCCCGGTGCCGGAAGGTTAATTGATGGGGTCAAGTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAATGATGGCCAGGCTGTCTCCACCCGAGACTCAGTGAAATTGAACTCGC TGTGAAGATCAGTGTACCCGCGGCAAGACGGAAGACCCCGGAACCTTTACTATAGCTTGACACTGAACATTGAGCCTTGATGTGTAGGATAGGTGGGAGG CTTAGAAGTGTGGACGCCAGTCTGCATGGAGCCACCTGAAATACCACCCTTTAATGTTTGTGTTCTAACGTTGATTTGCGGACAGTGTCTGGTGGGTAGT TTGACTGGGGCGGTCTCCTCCTAAAGAGTAACGGAGGAGCACGAAGGTTGGCTAATCCTGGTCGGACATCAGGAGGTTAGTGCAATGGCATAAGCCAGCT TGACTGCGAGCGTGACGCGGAGCAGGTGCGAAAGGGTCATAGTGATCCGGTGGTTCTGATGGAAGGGCCATCGCTCAACGGATAAAGGTACTCCGGGATA ACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGAAGTAGGCCCAAGGGTATGCTG TTCGCCATTAAAGTGGTACGCGAGCTGGGTTTAGAACGTGTGAGACAGTTCGGTCCCTATCTGCCGTGGGCGCTGGAGACTGAGGGGGCTGCTCCTAGTA CGAGAGGACCGGAGTGGACGCATACTGGTGTTCGGGTTGTCATGCCAATGCATGCCCGGTAGCTAAATCGGAGAGATAAGTGCTGAAACATCTAAGCACA AACTTCCCGAGAGAGTTCTCCCAGGAACGTTGAAGACGACACGTGATGGCCGG Ralstonia@solanacear CGAATAAGGCATGTGGTGGATGCCTTGGCGATCAGGCGATGAAGGACGCAGTAGTTGCGAAAAGCTGCGGGGAGCTGCAAAGAGCTTGATCCGCAGATGT CCGAATGTCTTCATGAGCGACGCAGTGACTGAAACATCTAAGTAGCTGCGGAAAAGAAATCAACGAGATTCCCAAAGTAGTGGCGAGCGAAATGGGATCA GCCTGTAGTTAGCAAAACGGAATGGAAATCCGGCCTAGTGGTGAAGCCCCGTAGCAAACGAAAGTGGGCGGGACACGTGAAATCCTGTCTGAAGATGGGG GGACCATCCTCCAAGGCTAAATACTCTGATCGACCGATAGTGAACAGTACCGTGAGGAAAGGCGAAAAGACCGGAGTGAAAAGTCTGAAACCGCATGCAT ACAACAGTCGGAGCCTAGGGTGACGGGTACCTTTTGTATAATGGGTCAGCGACTTACATTCAGTGGCAGCTTAACATGGAAGGCGTAGCGAGCGGTCCGA ATAGGGCGCAGTCGCTGGGTGTAGACCCAAACCAGTGATCTATCCATGGCCAGTTGAAGGTGCGTAACACGTACTGGAGGACCGAACACTAACGTTGAAA AGTTAGGGATGAGTGTGATAGGGGTGAAAGGCTAAACAAACTTGAAATAGCTGGTCTCTCCGAAAACTATTTAGGTAGTGCCTCGTGCACCTTCGGGGTA GAGCACTGTCATGGTTGGGGTTGATTACGCCATAGCAAACTCCGAATACCGATGCACGGGAGACAGACTCGGGTGCTAACGTCCGGTGTCAAGAGGGAAA CAACCCAGACCGCCAGCTAAGTCCCTAAGATGGCTAAGTGGAAACGAAGTGGAAGGCTAAAACAGTCAGGAGGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAATAGCTCACTGATCGAGTCGTCCCGGAAGATGTCGGCTAAGCCAGTCACCGAAGCTGCGGATTAATGGTAGGAGAGCGTTCTGTACCTGTAAGGTG TCTTGTGAGGATGCTGGAGGTATCAGAAGTGCGAATGTGACATGAGTAGCGAAAGGGGGTGAAAGGCCCCCTCGCCGTAAGCCCAAGGTTCCTACGCAAG TTCATCGGCGTAGGGTGAGTCGGCCCCTAAGGCGAGGCAGAACGTAGCTGATGGGAAGCAGGTAATATTCTGCACGGGACGGATGCGGAAGGTTGCCGGT TGGCCGGAATTAGTTCCAAGAAAAGCACCGTACCAAACCGACACAGGTGGGCAGATGAGTATTCTAAGGCGTTGAGAGAACTCGGGAGAAGGAACTCGGC AAATTGGTACCGTAACTTCGGGATAAGGTACGCCCTCGAGGTTGCAATAAAAGGTGGTGGACTGTTTAATAAAAACACAGCCTCTGCAAACACGAAAGTG ACGTATAGGGTGTGACGCCTGCCCGGTGCCGGAAGATTAAATGATGGGGTCAAGTCTTGATTGAAGTCCCGGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGATGGCCACACTGTCTCCTCCCGAGACTCAGCGAAGTTGAAGTGTT TGTGATGATCAATCTCCCCGCGGCTAGACGGAAGACCCCAGAACCTTTACTGTAGCTTTGCATTGGACTTTGAACCGATCTGTGTAGGATAGGTGGGAGG CTTTGAAACCGGGACGCTAGTTTCGGTGGAGCCTCCTGAAATACCACCCTGGTTTGTTTGGGTTCTAACCTTGATTCGGGGACAGTGCATGGTAGGCAGT TTGACTGGGGCGGTCTCCTCCCAAAGTGTAACGGAGGAGTTCGAAGGTACGCTTGGTACGGTCGGACATCGTACCTAAAGTGCAATGGCAAAAGCGTGCT TAACTGCGAGACCGACAGTGAGCAGGTGCGAAAGGGACATAGTGATCCGGTGGTTCTGATGGAAGGGCCATCGCTCAACGGATAAAGGTACTCTGGGATA ACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGGTTTGGCACCTCGATGTCGGCTCATCTCATCCTGGGGCTGTAGCCGGTCCAAGGGTATGCTG TTCGCCATTAAAGAGGTACGTGAGCTGGGTTTAAAACGTGTGAGACAGTTTGGTCCCTATCTGCCGTGGGCGTTGGAATTTGACGGGGCTGCTCCTAGTA CGAGAGGACCGGAGTGGACGTACGCTGGTGTACCTGTTGTCTCGCCAGAGCACGCAGGGTAGCTATGTCGGAGAGATAACCGCTGAAACATCTAAGCGGA AACTCCCTAAGAGAGGATTCCCAGGGTCGTTCGAGACCAGACGTGATGGCTGG Frankia@sp TTAGTAAGGCGCACGGTGGATGCCTTGGCACCAAGCCGATGAAGGACGTGGGAGCTGCGATATGCCTCGGGGAGCTGCAACGAGCTGGATCCGAGGATTT CCGAATGCCCACATGGGGGACGCGGGGAGTGAAACATCTCATTACCCGCGGAAGAGAAAACAACGTGATTCCGCGAGTAGTGGTGAGCGAAAGCGGATGA GGCTGGAGTTAGGCGAAGGTCATGCGAAGGGCGCCTAGAGGTAAAGCCCTGTACTAAACCCAAGTGCACGGAGCCCGTGAAATTCCGTGTGAATCTGGCG GGACCACCCGCTAAGCCTAAATACTCCTGGTGACCGATAGCGGATAGTACCGTGAGGAAAGGTGAAAAGTCCGGAGTGAAAAGACTGAAACCGTGTGCCT ACAACCGTGGGAGCTGCTGGTGACCGGTGCCTTTTGAAGAATGAGCCTGCGAGTTTGGATGTGTGGCGGGTTAACTGGGTAGCCGTAGCGAGCGGTCCGA AGAGGGCGGAGTCGCATGTCCAAGACCCAAGCCAGTGATCTACCCATGGCCAGTTGAAGCGCGGTAAGACCGTGTGGAGGACCGAACACCAGGGTTGAAA ACCTGGGGATGAGTGTGGTAGGGGTGAAAGGCCAATCAAACTCGTGATAGCTGGTCTCCCCGAAATGCATTTAGGTGCAGCGTCGCATTCTGCCGAGGTA GAGCACTGGATGGCCTAGGGCCCGCTAAAGTCAGCCAAACTCCGAATGCCGGAATGCGGCAGTGAGACGCGGGGGATAAGCTTCGTAGTCGAGAGGGAAA CAGCCCAGATCGCCAGCTAAGCCCCTAAGGGCGCTAAGTGGAAAGGATGTGAGTCGCATAGACAACCAGGAGGTTGCTTAGAAGCAGCCTTGAAAGAGTG CGTAATAGCTCACTGGTCAAGTGATTCCCGACAATGTCGGCTAAGCGCACCGCCGAAGCTGCGGCATTTGGGTAGGGGAGCGTCGTGTGCGTGTAAGCGG CGGGGTGACTGTCGTGGATGCCATACGAGTGAGAATGAGGCATGAGTAGCGATGACGGGTGAGAAACCCGTCCGCCGGATGACCAAGGTTCCTGGGGCAG CTAATCCGCCCAGGGTGAGTCGGGACCTAAGGCGAGGCCGAACGTAGTCGATGGACAACGGGTGATATTCCGTACGTGACGCAGAGGGTAGTCCACCAGG TGGCTGGGGATCCTGCCGAGAAAAGCCCCGTACCAAACCGACACAGGTGGTCGGTAGAGAATACCGAGGCGTCGAGTGAACTGTGGTTAAGGAACTCGGC AAAATGCCCCCGTAACTTCGGGAGAAGGGGGGCCGTTTATGCCGCAGAGACCGGGGAAGGACTGTTTACTAAAAACATAGCCCGTGCTAAGTCGTAAGAC ATGTATACGGAGTGACGCCTGCCCGGTGCTGGAACGTTAAGGGGACGGGTTCGGTCAGAACTTAAGCGCCAGTAAACGGCGGTGGTAACTATAACCATCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTTCCCACTGTCTCAACCACAGACTCGGCGAAATTGCATTACG AGTAAAGATCTCGTTACGCGCGGCAGGACGGAAGACCCCGGGACCTTTACTATAGCTTGATATTGGTGTTCGGTTCGGCTTGTGTAGGATAGGTGGGAGA CTGTGAAGCTGGGACGCCAGTTCTGGTGGAGTCTTGTGAAATACCACTCTGGTCGTACTGATGTCTAACCTCGATTCAGGGACAGTGTCTGGTGGGTAGT TTAACTGGGGCGGTTGCCTCCTAAAGAGTAACGGAGGCGCCCAAAGGTTCCCTCAGCCTGGTTGGCAATCAGGTGTTGAGTGCAAGTGCACAAGGGAGCT TGACTGTGAGACAGACAGTGAGCAGGTGCGAAAGGGGACTAGTGATCCGGCGGTGGCTGTGGAAGCGCCGTCGCTCAACGGATAAAGGTACCCCGGGATA ACAGGCTGATCTTGCCCAAGAGTCCATATCGACGGCAAGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGTAGGTCCAAGGGTTGGCTG TTCGCCCATAAAGCGGTACGCGAGCTGGGTTTAGAACGTGTGAGACAGTTCGGTCCCTATCCGCCGCGCGCGCAGGAGATTGAGAAGGCTGTCCCTAGTA CGAGAGGACCGGGACGGACGAACTCTGGTGTGCCAGTTGTTCTGCCAAGGCAGGCTGGTTGGCTACGTCGGAGGGATAACCGCTGAAACATCTAAGCGGA AGCCTCTTGAGAGAGGTCTCCCAGGCCCCCGATAGATGATGGGTGATGGCCGG Rhodopseudomonas@pal TGCTTAAGGTGTTCGACGGATGCCTTGGCGCTGAGGCGATGAAGGACGTGCTACCTGCGATAAGCCATGGGGAGCTGCGAAAAGCTTGATCCGTGGATTT CCGAATGGAGACATCAGCGACCCAGGGACTGAAACATCTAAGTACCTGGGGAAAGGACATCAACGAGACTCCGCTAGTAGTGGCGAGCGAACGCGTACCA GGCCATCACAATTGGAATCTGTAGGAAACAGAGCCTAGAGGTGAAGCCCCGTAAAAATGCTGAGTAGGCGGGACACGTGAAATCCTGTCTGAACATGGGG GGACCACCCTCCAAGCCTAAGTACTCTCAGCGACCGATAGTGAACAGTACCGTGAGGAAAGGTGAAAAGCCCGGAGTGAAAAGTCTGAAATCGGACACCT ACAACAGACGGAGCCCCGGGTGACGTGTACCTTTTGTATTATGGGCCAGCGACTTAATTTAACGAGCAGCTTAAGGTGGTAGGCGCAGCGAGCGGTCTGA ATAGGGCGAAGTTCGTTGGATTAGACCCAAACCAGTGATCTAGCCATGAGCAGTTGAAGGTGAGTAACACTCACTGGAGGACCGAAGGTGCCTGTTGAAA AAGGCCCGATGACTGTGTTAGGGGTGAAAGGCCAATCAAACTGGAAATAGCTGGTCTCCGCGAAAGATATTTAGGTATCGCCTCGGATACCTCAGGGGTA GAGCACTGGATGGGCTAGGGATCTCTAAACCCAACCAAACTCCGAATACCTGTATCCGGGAGTCACACGCGGGTGCTAACGTCCGTCGTGGAGAGGGAAA CAACCCTGACCTACAGCTAAGCCCCCAATCTGGCTAAGTGGAAAGGATGTGAAATCCCAAAACAACCAGGAGGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAACAGCTCACTGGTCTAGGGTTTCCCGAAGATGTCGGCTAAGCCACGAGCCGAAGCTTAGGGTCAGCGGTAGCGGAGCGTTCTGTACCTGCAAGGGG ACCCGTGAGGCGCCTGGAGGTATCAGAAGTGCGAATGTGGCATGAGTAACGAAACACTGTGAAAGACAGTGTCGCCGAAAGTCCAAGGTTCCTGCGTAAG TTAATCTTCGCAGGGTTAGCCGGTCCCTAAGGCGAGGCCGAACGTAGTCGATGGGAATCACGGAATATTGTGAGCGTGACGAATCCCTTAGTTGTCGACA CTGGTCGCCTCGGTTCCAGGAAATACACCGTACCAAACCGACACAGGTGGACGGTAGAGTATACCAAGGCGTTGAGAGAACTATGTTGAAGGAACTCGGC AATTTACCTCCGTAACTTCGGGATAAGGAGGCCTTCCAAGGGGGCACAGACCGGGGGGGAACTGTTTAACAAAAACACAGGCTCTGCGAAATCGCAAGAT ACGTATAGGGTCTGACGCCTGCCCGGTGCCGGAAGGTTAAGAGGAGGAGTCAAGTCTGAATTGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAATGACTTCCCCGCTGTCTCCAACATAGACTCAGTGAAATTGAATTCCC CGTGAAGATCGGGGTTCCTGCGGTCAGACGGAAGACCCCGGCACCTTTACTGTAGCTTTGCGCTGGTATTCGTGACTGTTTGTGTAGAATAGGTGGTAGG CTTTGAAGCTCGGGCGCCAGCTCGGGTGGAGCCCAATGAAATACCACCCTAATGGTTATGATATCTAACCGCGATTCCGGGACAGCGCATGGTGGGCAGT TTGACTGGGGCGGTCGCCTCCCAAAGAGTAACGGAGGCGTGCGACGGTAGGCTCAGAACGGTCGGAAATCGTTCGTCGAGTACAATGGCATAAGCCTGCC TGACTGCGAGACCAACAGTGAGCAGAGACGAAAGGGTCATAGTGATCCGGTGGTCCCGGTGGATGGGCCATCGCTCAACGGATAAAGGTACGCCGGGATA ACAGGCTGATGACGCCCAAGAGTCCATATCGACGGCGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGGAGAAGGTCCAAGGGTTCGCTG TTCGCCGATAAAGTGGTACGTGAGCTGGGTTCAGAACGTGTGAGACAGTTCGGTCCCTATCTGCCGTGGGTGTTGGAATTTGAGAGGATTGCCCCTAGTA CGAGAGGACCGGGGTGAACGTACTCTGGTGGAGCTGTTGTCGCGCCAGCGCATGCAGCATAGCTATGTCGGCGGGATAACCGCTGAAACATCTAAGCGGA AACCCCCTAAAAGAGCATTCCCAGAACCGTGGAAGACCACACGTGATGGCCGG Chlamydia@muridarum TTGATAAGGCTATTGGTGGATGCCTTGGCATTGAGGCGATGAAGGACGCGAATACTGCGAAAAGCTCCGGCGAGCTGGTAAAAGCAAGACCCGGAGGTGT CCGAATGTTGACATAAGCAACCTGCTGACTGAAACATCTTAGTAAGCAGGGAAAAGAAATCGAAGAGATTCCCTGTGTAGCGGCGAGCGAAAGGGGAAGA GCCTGGACCTAGTTGAACCATCTGGAAAGTGGATGAACAGGTGAAGTCCCGTAACAAGCCTGAGTGGGCTAGACACGTGAAACCTAGTCTGAATCTGGGG AGACCACTCTCCAAGGCTAAATACTATCAATGACCGATAGTGAACAGTACTGTGAAGAAAGGCGAAAAGACTTGAGTGAAAAGACTGAAACCAGTAGCTT ACAACGGTCGAAGACCAGGTTGACGGGTGCCTTTTGCATGATGAGCCAGGGAGTTAAGCTAAACGGCGGGTTAAGTACGGAGCCGAAGCGAGCGGTTTTA AAAGAGCGTAGTCGTTTGGTTTAGACACAAACCAGTGAGCTATTTATGACCAGTTGAAGCATGGTAAAACTATGTGGAGGACCGAAAGTACCTGTTGAAA AAGGTTGGATGAGTGTAATAGGGGTGAAAGGCCAATCAAACTTGAGATATCTTGTCTCTCCGAAATAACTATAGGGTTAGCCTCGGAAATTTTTGGGGTA GAGCACTGAATTCTAGCGGGCTCGCTAACGGAAATCAAACTCCGAATACCAAGATCCGGGAGATAGACGCGGGGGCTAAGCTTCGTTGTCGAGAGGGGAA CAGCCCAGACCGCCGATTAAGTCCCTAATTATGCTAAGTGATAAGGAAGTATGATTCTAAGACAGTTGGAATGTTGCTTAGAGGCAGCATTTAAAGAGTG CGTAACAGCTCACCAATCGAGAATCATCCGATAATAACGGCTAAGCATAAAACCGACATCGCGGGTTTGCGGTAGGAGAGCGTAGTATTGCAGTAAGGTG TACCGGAAGAGCGCTGGAGCGGATACTAGTGAAGATCTGGCATAAGTAACGAAAGGGAGTGAAAATCTCCCTCGCCGTAAGCCCAAGGTTCCAGGGTCAG CTCGTCTTCCCTGGGTTAGTCGGCCCCTAAGTCGAGGCGTACCGTAGACGATGGACAGCAGGTAATATTCTGCACATGACGGAGAAGTTAAGCACCGGAT TGGTCCGGTGTCCTTTCAAGAAATATACCGTACCAAACCGACACAGGTGGGCAGATGAGTATTCTAAGGCGGCGAGATAACTTTCGTTAAGGAACTCGGC AAATTATCCCCGTAACTTCGGAATAAGGGGAGCCTTGAGGGCCGCAGAGAAAGGCCCGGGACTGTTTAGCAAAAACACAGCCTATGCAAACCTCTAAGGG AAGTATATGGTGTGACGCCTGCCCAATGCCAAAAGGTTAAAGGGATATGTCAAGATTGAACCTAAGCCCTGGTGAATGGCCGCCGTAACTATAACGGTGC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGTGTAACGATCTGGGCACTGTCTCAACGAAAGACTCGGTGAAATTGTAGTAGC AGTGAAGATCTGTTTACCCGCGAAAGGACGAAAGACCCCGGAACCTTTACTGTACTTTGGTATTGATTTTTGGTTTGTTATGTGTAGGATAGCCAGGAGA CTAAGAACACCCTTCGTCAGGAGGGTGGGAGTCACGTGAAATACTGGTCTTAACAAGCTGGAATCTAACATTAATAGATGGACATTGCCAGACGGGCAGT TTTACTGGGGCGGTATCCTCCTAAAAAGTAACGGAGGAGCCCAAAGCTTATTTCATCGTGGTTGGCAATCACGAGTAGAGCGTAAAGGTATAAGATAGGT TGACTGCAAGACCAACAGTGAGCAGAGACGAAAGGGGCTTAGTGATCCGGCGGTGGAAGTGGAATCGCCGTCGCTTAACGGATAAAGGTACTCCGGGATA ACAGGCTGATCGCCACCAAGAGTTCATATCGACGTGGCGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGGGCTGGAGAAGGTCCAAGGGTTTGCTG TTCGCCAATAAAGCGGTACGCGAGCTGGGTTCAAAACGTGTGAGACAGTTTGGTCTCTATCCTTCGTGGGCGCAGGATATTGAGAGGACTGTTCCTAGTA CGAGAGGACCGGAATGGACGAACAATGGTGTGTCGGTTGTTTTGCCAAGACAAGCCGAGTAGCTAAGTCGGAAGGATAAGCATTGAAACATCTAAATGCA AGCCTCCTAAGAAAGGTATCCCAGACTCCATGTAGACTACTGGTGATGGTTGG Leuconostoc@lactis TTAATAAGGCGCGTGGTGGATGCCTTGGCACTAAGCCGATGAAGGACGTGACTAACACGATAAGCTTTGGTGAGCGGTAAGACGCTAGACCCAGAGATTT CCGAATGTCAACATGAGAAACGCTGTGACTGAAACATCTCATTAGCAGCGGAGAAGAAAGAAAATCGATTCCCTAAGTAGCGGCGAGCGAACGGGGAAGA GCCCGGATATAGCAGAACAAGTTGGGAACTTGGCTTAGAGGTGAAGCCCCGTAGCAATCCTGAGTCGGCCGGACACGTGAAATCCGGTCGGAATCTGCGG GGACCATCCCGTAAGGCTAAATACTCCTAGTGACCGATAGTGAACAGTACCGTGAGGAAAGGTGAAAAGCCCGGAGTGAAAAGTCTGAAACCAGACGCCT ACAAAAGTCAGAGCCCAGGGTGATGGGTGCCTTTTGTAGAATGAACCGGCGAGTTACGGTATCGTGCGGGTTAAGAACGGAGCCGCAGCGAGCGGTGTGA ATAGCGCGTAGTACGATGCTGTAGACCCAAACCAGTGACCTACCCATGGTCAGATGAAGGTGAGTAAAACTTACTGGAGGTCCGAAGGTGCATGTTAAAA AATGCCGGATGAATGTGGTAGCGGTGAAATTCCAAACGAACTTGAGATAGCTGGTCTCTCCGAAATAGCTTTAGGGCTAGCCTCGTAAGGTACTGAGGTA GAGCTCTGTTTGGACTAGGCCTAGGTAAATTCAGATAAACTCCGAATTCCAGCACACGGGAGTCAGACGCGAGTGATAAGATCCGCAGTCGAAAGGGAAA CAGCCCAGATCACCAGTTAAGTCCCAAAAAATGCTAAGTGGAAAGGATGTGAGTTGCGCAGACAACTAGGATGTTGCTTAGAAGCAGCCTTCAAAGAGTG CGTAATAGCTCACTAGTCGAGTGACGCCCGAAAATTTCGGCTAAGCATATTACCGAAACTGTGGGTTAGCGATAGGAGAGCGTTGTAAGGCGATAAGGGA GATCGTAAGACTGCTGGAGCGCTTACAAGTGAGAATGCGGTATGAGTAGCGAAGACAGGTGAGAATCCTGTCCACCGAATGACTAAGGTTCCTGGGGAAG CTCGTCCACCCAGGGTTAGTCGGGACCTAAGGCGAGGCTGAACGTAGTCGACGGATAACAGGTGAGATTCTGTACGGGACGCAGAGGCTACCAGACGCAA TGGTGCGCTGCCCTGCCGAGAAAAGCCCCGTACCAAACCGACACAGGTAGTCAGTGGAGAACACTAAGGTGGCGAGAGAACCCTCGTTAAGGAACTCGGC AAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCACATAGCCGCAGTGAATGGCCCAGGACTGTTTATCAAAAACACAGGTTCTGCAAAATCGTAAGAT AAGTATAGGGGCTGACGCCTGCCCGGTGCTGGAAGGTTAAAAGGAGTGCTTCGGTACGAATTGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCCGCACGAAAGGCGTAACGATCTGGGCACTGTCTCAACGAGGGACTCGGTGAAATTTAAATACC CGTGAAGATCGGGTTACCCGCGACAGGACGGAAGACCCCAGGAGCTTTACTGTAGCTTGATATTGAATGTTTGTGCTGCTTGTACAGAATAGGTAGGAGA CGAAGAAATTTGGACGCCAGTCTAGACGGAGTCAATTGGGATACTACCCTCGTTGTATGACATTCTAACACTGATTCGTGGACAGTGTCTGGCGGGCAGT TTGACTGGGGCGGTCGCCTCCTAAAAGGTAACGGAGGCGCTCAAAGGTTTGCTCAGAATGGTTGGAAATCATTCGTAGCGTGTAAAGGCATAAGCAAGCT TGACTGCGAGAGTTACACTGAGCAGGTACGAAAGGGACTTAGTGATCCGGTGGTTCCGATGGAAGGGCCATCGCTCAACGGATAAAGCTACCCTGGGATA ACAGGCACATCTCCCCCAAGAGTCCACATCGACGGGGAGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGGGCTGTAGTCGGTCCAAGGGTTGGCTG TTCGCCCATAAAGCGGTACCCGAGCTGGGTTCAGAACGTGTGAGACAGTTCGGTCCCTATCCGTCGCGGGCGCAGGAAATTGAGAGGACTGTCCTTAGTA CGAGAGGACCGGGATGGACATACGCTGGTGTACCAGTTGTTCCGCCAGGACATGCTGGGTAGCTATGTTGGTGAGATAAACGCTGAAACATCTAAGTGTA AACTCCCTGAGAGAGATTTCCCAGACCCCTTAGAGATGATAGGTGATGGCTAG Micrococcus TTTCCAAGGCGCATGGTGGATGCCTTGGCAACAAGCCGAAGAAGGACGTGGGAACTGCGATAAGCCTGGTGGAGTCGTAACGGACGTGAGACCAGGATTT CCGAATGCCCACATGGGGGACGTGGGGACTGAAACATCTCAGTACCCACGGAAGAGAAAACAAAGTGATTCCGTTAGTAGTGGCGAGCGAACGCGGATGG GGCTGGCTATAGACGAACCAGTGTGGATCTGGACCTAGAGGTGAAGTCCCGTATCAATCCCGAGTGCACGGGGCCCGAGGAATCCCGTGTGAATCTGCCA GGACCACCTGGTAAGCCTGAATACTACTGTTGACCGATAGCGGACAGTACCGTGAGGAATGGTGAAAAGTCCGGAGTGAAAAGACTGAAACCATGTGCCT ACAACCGTTGGAGCCTTGGGTGACAGGTGCCTTTTGAAGAATGAGCCTGCGAGTTAGGATACGTGGCGGGTTAACTGGGAAGCCGTAGCGAGCGGTCTGA ATAGGGCGGAGTCGCGTGTCCTAGACCCAAGCGAGTGATCTACCCATGGCCAGTTGAAGCGCGTTAAGAACGCGTGGAGGACCGAACACTTCAGTTGAAA ATGGAGGGATGAGTGTGGTAGGGGTGAAAGGCCAATCAAACTCGTGATAGCTGGTCTCCCCGAAATGCATTTAGGTGCAGCGTCACGTTCTCCCGAGGTA GAGCACTGGATGGACGAGGCCTCGGCAACTTCAGCCAAACTCCGAATGCCGGAGCGTGGCAGTGAGACGTGGGGGATAAGCTTCATAGTCGAGAGGGAAA CAGCCCAGACCACCGGTTAAGCCCCTAAGGGTGCTAAGTGGAAAGGATGTGAGTTGCTGAGACAACCAGGAGGTTGCTTAGAAGCAGCCTTGAAAGAGTG CGTAATAGCTCACTGGTCAAGTGATTCCCGACAATGTCGGCTAAGTACACCGCCGAAACCGTGGCATTTGGGTAGGGGAGCGTCGTTCAGAGGTAAGCCA GCGGGTAATTCTGGTGGATTGTGGACGAGTGAGAATGAGGCATGAGTAGCGAAGACGGGTGAGAAACCCGTCCGCCGGATGACTAAGGTTCCAGGGTCAG CTAATCTGCCCTGGGTAAGTCGGGACCTAAGGCGAGGCCGAACGTAGTCGATGGACAACGGGTGATATTCCGTACGTGACGCAGAAGGTAGCCGGCCGGA TGGCTGGCGGTTCTGCCTAGAAAAGCCCCGTACCAAACCGACACAGGTGGTCGGTCGAGAATACTAAGGCGTCGAGAGAATCATGGTTAAGGAACTCGGC AAAATGCCCCCGTAACTTCGGGAGAAGGGGGGCCCCGTCGGCCGCAGAGACCGGGGGAGGACTGTTTATCAAAAACACAGGCCATGCGAAGTCGTAAGAC ATGTATATGGACTGACTCCTGCCCGGTGCTGGAAGGTTAAGGGGACCCGTTCGGGGAGAACTTAAGCCCCAGTAAACGGCGGTGGTAACTATAACCATCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGAGTAACGACTTCCCCGCTGTCTCAACCATGAACTCGGCGAAATTGCATTACG AGTAAAGATCTCGTTACGCGCAGAAGGACGGAAGACCCCGTGACCTTTACTATAGTTTGGTATTGGTGTTCGGTGTGGCTTGTGTAGGATAGGTGGGAGA CTGTGAAGCGGGCACGCCAGTGTTCGTGGAGTCTCGTGAAATACCACTCTGGTCACTCTGATATCTAACTTCGATTCAGGGACAGTGCCTGATGGGTAGT TTAACTGGGGCGGTTGCCTCCTAAAATGTAACGGAGGCGCCCAAAGGTTCCCTCAGCCTGGTTGGTAATCAGGTGTCGAGTGCAAGTGCACAAGGGAGCT TGACTGTGAGAGTGGCACTGAGCAGGGACGAAAGGGGACTAGTGATCCGGCGGCTCGTGTGGAACGGCCGTCGCTCAACGGATAAAGGTACCTCGGGATA ACAGGCTGATCTTGCCCAAGAGTCCATATCGACGGCATGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGTAGGTCCAAGGGTTGGCTG TTCGCCCATAAAGCGGTACGCGAGCTGGGTTCAGAACGTGTGAGACAGTTCGGTCCCTATCCTCTGCGCGCGTTGGAAATTGAGAAGGCTGTCCCTAGTA CGAGAGGACCGGGACGGACGAACTCTGGTATGTCAGTTGTACCGCCAGGTCAGGCTGATTAGCTACGTCGGATGGATAACCGCTGAAACATCTAAGCGGA AGCCGCTTGAGAGAGATTTCCTAGGCCCCCAGTAGAACACGGGTGATGGCTGG Treponema CGAATAGTGTTTACGGTGGATGTCTTGGAGTTGAGGCGATGAAGGTCGTGATAACTGCGAAAAGCCTCGGGGAGGAGCACAGTCCTGGATCCGGGGATGA CCGAATGTTGGAATAACGAACTGGGTGACTGAACCATCTAAGTAACTTGGGAAAAGAAATCAAGGAGATTCCGAAAGTAGTGGCGAGCGAAATTGGAGGA GCCTGGGTATAGCAGAAAGGTTTGGGAAGCCTGACGAGAGGTGAATCCCCGTAGCAATCCTGAGTCGGCGGGACACGAGGAATCCTGTCGGAATCTGGGT CGACCACGATCTAAGGCTAAATACTCACAACTACCGATAGTGGAAAGTACCGTGAGGAAAGATGAAAAGACCGGAGTGAAAAGACTGAAACCGTAAACCA ACAAATGTTACAGCCTGGGGTGGTAGGTGCCTTTTGTAGAATGAGCCTGCGAGTTACGGTGTGCAGCAGGTTAAGGGCGGAGCCGGAGGGACCGGTCTTA AAAGGGCGGAGTTGTACGTCGTAGACCCAAGCCGGTGATCTAGTTATGAGCAGTTGAAACAGGGTGAAGCCTTGTGGAGGACCGAAATAATCTGTTAAAA AAGGTTGGATGACTGTACTAGGAGTGAAAGGCTAAACAAACCTGAGATAGCTGGTCTCCCCGAAATGCCTTTAGGGACAGCCTTATAAACTGTCGAGGTA AAGCACTGGATGGGCTAGGGTTAGCCAAACCCAATCAAACTCTGAATGCCGGTCTGTGGGAGTGAGACGCGTGCGACAAGGTTCGTAGTCGAGAGGGAAA CAGCCCAGACCGTCAGCTAAGTCCCGAAAACGCTTGAGTGTAAATGAAGTTGGGTACCTGGACAGCCAGGAGGTTGCTTAGAAGCAGCCTTGAAAGAGTG CGTAATAGCTCACTGGTCGAGTACGCACAGATAATGTCGGCTAAGCGGTATACCGAAGCTACGGGTTTGCGGTAGGGGAGCATTCCATGCTGATAAGGAT ATCCGGGAGAGTTCTGGAGGGGATGGAAGAGAGAATGAGGTATAAGTAACGAAGGAGGGTGAGATTCCTTCCCGCCGAAAACCTAAGGTTCCTGGGTGAG GTCATCTGCTCAGGGTAAGTCGGCCCCTAAGGCGAGGACGAGCGTAGTCGATGGGAATCCGGTTATATTCGGAACAGGACGCGTAGGTGAAGCCCGCCAT TGGTTGGAGGTCGCGACGGGAAATATACCGTACCAAACCGACACAGGTAGGTGGATGAGTAATCTAAGGCGTCGAGAGAACTCGCGTCAAGGAACTCGGC AAAATACACACGTAACCTCGGGAGAAGTGTGACCCTTTGGGTGGCAGAAAGCGGTCCGGGACTGTTTATCAAAAACATAGCATCTGCAAATCAGTAATGA ACGTATAGGTGGTGACACCTGCCCGGTGCTGGAAGGTTAAGAGGAGAGGTTAAGTTTGAATTGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCCGCACGAATGGTGTAACGACTCTGGAACTGTCTCGACGCGAGACTCGGTGAAATTTATGTACC GGTAAAGAACCGGTTACCCATAGTTAGACGGAAGACCCCGGAACCTTCACCGTAGCTTACTATTGGAACTTGGTTTACCATGTGTAGTATAGGTGGGAGA CAGAGAAGCTTGGCCGTCAGGTTAGGCGGAGTCACATGAAATACCACCCTTGGTACGTCAGTTTCTAACCTTTGAAAAGGGACCGTGGTAGGTGGGCGGT TTGACTGGGGCGGTCGCCTCCTAAAAGGTAACGGAGGTGCGCGAAGGTCTCCTCACACCGGTTGGAAATCGGTGCGCGAGTGTAAAGGCACAAGGAGGCT TAACTGCGAGACCGACAGTGAGCAGATACGAAAGGGTCTTAGTGATCTGGCGGTAGCGGTGGAAGCGCCGTCACTTAACGGATAAAGGTACTCCGGGATA ACAGGCTGATTTTCCCCAAGAGTTCACATCGACGGGAAGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGGGCTGAAGCAGGTCCAAGGGTTTGCTG TTCGCCAATAAAGCGGTACGTGAGCTGGGTTCAGAACGTGCGAGACAGTTCGGTCCCTATCTGCTATGGGCGTTGGATAGTGAGAGGACTGCTTTTAGTA CGAGAGGACCGAAGTGGACGAACTCTGGTGTACCAGTTATCCTGCCAAGGTATGCTGGGTAGCTATGTCGGAGGGATAACCGCTGAAGCATCTAAGTGGA AGCCCCCTAAGATACATATCCCAGACTCCTTGCACACTACAGGTGATGGCTGG Zoogloea TGCGTAAGGCAATTGGTGGATGCCTTGGCATGCAGGCGATGAAGGACGTGATACCTGCGATAAGCCGTGGGGAGCTGCGAAGAGCTTGATCCATGGATTT CCGAATGTCTACATGAGCGACGCAGGGACTGAAACATCTAAGTACCTGCGGAAAGGACATCAACGAGACTCCGCAAGTAGTGGCGAGCGAACGCGGACCA GGCCGCATAAAGTGGAACGGAATGGAAATCCGGCCTAGCGGTGAAGCCCCGTAACAGACCTGAGTGGGCGGGACACGTGAAATCCTGTCTGAACATGGGG AGACCACTCTCCAAGCCTAAGTACTCTGCATGACCGATAGCGAAAAGTACCGTGAGGAAAGGTGAAAAGCCCGGAGTGAAAAGACTGAAACCGGTTGCCT ACAACAGTCGGAGGCCAGGCTGACGGGTACCTTTTGTATAATGGGTCAACGACTTAGTGTAACTAGCAGCTTAAGGTGGTAGGCGCAGCGAGCGGTCTGA ACAGGGCGCAGTTAGTTGCATTAGACCCAAACCAGTGATCTAGCCATGAGCAGTTGAAGGTTGGTAACACCAACTGGAGGACCGAACGCATCTGTTGCAA TAGATGGGATGACTGTGCTAGGGGTGAAAGGCCAATCAAACTCGAGATAGCTGGTCTCCGCGAAATCTATTTAGGTAGAGCGTCGACTACCCTCGGGGTA GAGCACTGGATGGGCTAGGGACCTCTAATCCTAACCAAACTCCGAATACCGATAGTCGGCAGACACACGCGGGTGCTAACGTCCGTCGTGAAAAGGGCAA CAACCCTGACCTCCAGCTAAGTCCCCAAGCTGGCTAAGTGGAAAGGATGTAGACTCCCAAAACAACCAGGATGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAACAGCTCACTGGTCTAGGGGTTTCCGAAAATGTCGGCTAAGCCATGCACCGAAGCTGAGGATCAGTGGTAGCGGAGCGTTCCGTACCTGCAAGGAG GACCCGTGGGCCTCTGGAGGTATCGGAAGTGCGAATGTGACATGAGTAACGAAAGGGAGTGAGAGACTCCCTCGCCGAAAGACCAAGGTTCCTGCTTAAG TTAATCTGAGCAGGGTTAGCCGGCCCCTAAGACGAGGCGGAACGTAGTCGATGGGAACCACGTAATATTGTGGGCGTGACGGATTGCGTACTTGTCATCA TTGGGTGCAGGGGTTCCAGGAAATACACCGTACCAAACCGACACAGGTGGTCGGTAGAGCATACCAAGGCGTTGAGAGAACTGCGTTGAAGGAACTCGGC AAATTGCACGCGTAACTTCGGAAGAAGCGTGACCCCCATGGTGGCACAGACCGGGGGAGGACTGTTTATCAAAAACACAGGCTCTGCGAAGTCGCAAGAC ACGTATAGGGTCTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGAGAGGTCAAGTTTGAATCGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCCCCGCTGTCTCCAACGCAGACTCAGTGAAATTGAATTCCC CGTGAAGATCGGGGTTCCTGCGGTTAGACGGAAGACCCCGGCACCTTTACTATAGCTTTACACTGGCATTCGTGTCGGCATGTGTAGGATAGGTGGTAGG CTTTGAAGCAGGGACGCCAGTTTCTGTGGAGCCTCCTGAAATACCACCCTTATCGTCATGATGTCTAACCGCGATTCCGGGACCGTGTATGGTGGGTAGT TTGACTGGGGCGGTCGCCTCCGAAAGAGTAACGGAGGCGCGCGATGGTGGGCTCAGACCGGTCGGAAATCGGTCGTCGAGTGCAATGGCATAAGCCCGCC TGACTGCGAGACTGACAGTGAGCAGAGACGAAAGGGTCATAGTGATCCGGTGGTCCCGGTGGAAGGGCCATCGCTCAACGGATAAAGGTACGCCGGGATA ACAGGCTGATGACCCCCAAGAGTCCATATCGACGGGGTGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGGGCTGGAGCAGGTCCAAGGGTTTGCTG TTCGCCAATAAAGCGGTACGTGAGCTGGGTTCAGAACGTGTGAGACAGTTCGGTCCCTATCTGCCGTGGGTGTAGGAATTTGACAGGACTGTCCCTAGTA CGAGAGGACCGGGATGGACATATTCTGGTGGACCTGTTGTCCTGCCAAGGCAAGCAGGGTAGCTATATTGGATGGATAACCGCTGAAGCATCTAAGCGGA AACCACCTAAAACGAGTATTCCAGAGCCGTGGAAGACGACACGTGATGGCCGG Renibacterium TTTTTAAGGCACACGGTGAATGCCTTGGCATTAAGCCGAAGAAGGACGTAGGAACTGCGATAAGCCTCGGGGAGTTGTAACGAACACGATCCGAGGATGT CCGAATGCCCACATGGGGGACGTGGGGACTGAAACATCTCAGTACCCACGGAAGAGAAAACAATGTGATTCCGTAAGTAGTGGCGAGCGAACGCGGAACA GGCTGGACATAGGTGAACGGTCTTGAAAGCCGGCCGAGAGGTGTAGCCCCGTACTAATCCCAAGTGCACGGGGCCCGAGAAATCCCGTGCGAATCTGTCA GGACCACCTGATAAGCCTAAATACTCCTAATGACCGATAGCGGAAAGTACCGTGAGGAAAGGTGAAAAGTCCGGAGTGAAAAGACTGAAACCGTGTGCTT ACAACCGTCGGAGCAGTCTGTGACGGGTGCCTTTTGAAGAATGAGCCTGCGAGTTAGGCTCAGTGGCGGGTTAACTGGGCAGCCGTAGCGAGCGGTCTGA ATAGGGCGGAGTCGCTGGGTCTAGACCCAAGCGAGTGATCTACCCATGGCCAGTTGAAGCGACGTAAGACGTCGTGGAGGACCGAACACTTCAGTTGAAA ATGGAGGGATGAGTGTGGTAGGGGTGAAAGGCCAATCAAACTCGTGATAGCTGGTCTCCCCGAAATGCATTTAGGTGCAGCGTTGCGTTCTACTGAGGTA GAGCACTGGATGGCCGAGGCCTCGGTAACGTCAGCCAAACTCCGAATGCCGGAGCGCAGCAGTGAGACGTGGGGGATAAGCTTCATAGTCGAGAGGGAAA CAGCCCAGACCACCAACTAAGTCCCTAAGGGTGCTAAGTGGAAAGGATGTGGATTGCTTAGACAACCAGGAGGTTGCTTAGAAGCAGCCTTGAAAGAGTG CGTAATAGCTCACTGGTCAAGTGATTCCCGACAATGTCGGCTAAGTACACCGCCGAAGTTGTGGATTCGTGGTAGGGGAGCGTCGTGTGGCAGTAAGTCG CGGTGTAACCGCGGTGGAGCCTACACGAGTGAGAATGAGGCATGAGTAGCGAAGACGGGTGAGAAACCCGTCCGCCGAATGATCAAGGTTCCAGGGTCAG CTAATCTGCCCTGGGTAAGTCGGGACCTAAGGCGAGGCCGAACGTAGTCGATGGACAACGGGTGATATTCCGTACGTGACGCAGAAGGTAGCTGACCGGA TGGCCGGCAGTTCTGCCAAGAAAAGCCCCGTACCAAACCGACACAGGTGATCGGTAGAGAATACTAAGGCGTCGAGAGAATTATGGTTAAGGAACTCGGC AAAATGCCCCCGTAACTTCGGGAGAAGGGGGGCCCCTTAGGCCGCAGAGACCGGGGGAGGACTGTTTACTAAAAACACAGGCCGTGCGAAGTCGCAAGAC ATGTATACGGACTGACTCCTGCCCGGTGCTGGAAGGTTAAGAGGACCGGTTCGGTGAGAATTTAAGCCCCAGTAAACGGCGGTGGTAACTATAACCATCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGAGTAACGACTTCCCCGCTGTCTCAACCATAAACTCGGCGAAATTGCACTACG AGTAAAGATCTCGTTACGCGCAGCAGGACGGAAGACCCCGAGACCTTTACTATAGTTTGGTATTGGTGTTCTAAGTGGTTTGTGTAGGATAGGTGGGAGA CTTTGAAGCCCGGACGCCAGTTCGGGTGGAGTCTCGTGAAATACCACTCTGGCCACTTGGACTCCTAACTTCGATTCAGGGACAGTGCCTGATGGGTAGT TTAACTGGGGCGGTTGCCTCCTAAAGAGTAACGGAGGCGCCCAAAGGTTCCCTCAGCCTGGTTGGCAATCAGGTGTCGAGTGTAAGTGCACAAGGGAGCT TGACTGTGAGAGCGACACTGAGCAGGGACGAAAGGGGACTAGTGATCCGGCGGTACATGTGGAATGGCCGTCGCTCAACGGATAAAGGTACCTCGGGATA ACAGGCTGATCTTGCCCAAGAGTCCATATCGACGGCATGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGTAGGTCCAAGGGTTGGCTG TTCGCCCATAAAGCGGTACGCGAGCTGGGTTTAGAACGTGTGAGACAGTTCGGTCCCTATCCGCTGCGCGCGCAGGAAATTGAGAAGACTGTCCTTAGTA CGAGAGGACCGGGACGGACGAACTCTGGTGTGTCAGTTGTACTGCCAAGTCACGCTGATTAGCTACGTCGGAGGGATAACCGCTGAAACATCTAAGCGGA AGCCCCTTAAGAGAGATTTCCAAGGCCCCCAGCAGACCACGGGTGATGGCCGG Ruminobacter TGAATAAGGTACATGGTGGATGCCTAGGCAATAAGGCGAAGAAGGACGTGCTAACTGCGAAAAGTCATGATGAGCTGGTAAAAGCCAAAGTCATGGATGT CCGAATGTCAGCAAGAGCGACCGGGAGAGTGAAACATCTCAGTACCCCGGGAAAAGAAATCAACGAGATTTCCTAAGTAGTGGCGAACGAACGGGAAGCA GCCCAAACATAGTTGAATTATCTGGAAAGTAAACGAAGAAGTGAAGTCTCGTAACAGTAAAGAGTGGACGGAACACGTGGAATTCTGTCTGAAGATAGGG GGACCATCCTCTAAGGCTAAATACTATTATTGACCGATAGTGAAAAGTACCGTGAGGAAAGGCGAAAAGACCTGAGTGAAAAGACTGAAACCGTGTACGT ACAACAGTGGGAGCACCGTGTGACTGGTACCTTTTGTATAATCGGTCAGCGAGTTACTTTCAGTGGCGGGTTAACCAGGGAGCCGAAGGGACCGGTTTTA ACTGAGCGGAGTCGCTGGGAGTAGACCCAAACCGATGATCTAGTCATGGGCAGATGAAGGCAAGTAACACTTGCTGGAGGGCCGAACACTAACGTTGCAA AGTTAGGGATGACTGTACTAGGGGTGAAAGGCCAATCAAATCAGTGATATCTGGTCTCCCCGAAAGCTATTTAGGTAGCGCCTCAAAAGTTATGGAGGTA GAGCACTGTTTCGATAAGGTCTCGATGAGTCGATGCAAACTCCGAATACTCAGATTTGGGAGACAGACGCGGGTGCTAAGGTCCGTTGTCGAGAGGGAAA GAGCCCAGACCGCCAGCTAAGTCCCGAAGTAGGTTAAGTGGAAACGATGTGGAAGGCATAGACAGCTAGGATGTTGCTTAGAAGCAGCCTTAAAAGAAAG CGTAATAGCTCACTAGTCGAGTCGGCCCGGAAGATGTCGGCTAAACCTTACACCGAAGCTGCGGAAAATTGGTAGGGGAGCGTTCTGTAGCTGTAAGGGC AACTGGAAGTTGACTGGAGCTATCAGAAGTGCGAATGTGACGTGAGTAACGAATATATGTGAAAAACATATACGCCGAAAGACCAAGGTTTCTGTCCAAG TTAATCGGGGCAGAGTGAGTCGGTACCTAATGTAAGGCTGAACGTAGACGATGGATATTCGGTAATATTCGAAACAGGACGGAGAGGCTAGTGCTCTTAT TGGTAAGGCATCCTTCCAGGAAAAGTGCCGTACCAAACCGACACAGGTGGTCGGTAGAGAATACCAAGGCGTTGAGAGAACTCGGGTGAAGGAACTAGGC AAAATAGTACCGTAACTTAGGGAGAAGGTATGCTGAGCACGTGACAGCAAAGGGTGGTGGACTGTTTAACAAAAACACAGCCACTGCGAACACGGAAGTG AAGTATAGTGTGTGACACCTGCCCGGTGCCGGAAGGTTAAATGATGAAGTCAAGTTCTGATTGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGCAAGTTCCGACCTGCACGAATGGTGTAACCATGGCCACGCTGTCTCCACCCGAGACTCAGTGAAATCGAAATCGC TGTGAAGATCAGTGTACCCGCGGCTAGACGGAAGACCCCGGAACCTTTACTATAGCTTGACACTGAACATTGAGTCTGTCTGTGTAGGATAGATGGGAGA CAGAGAAGCGAGTACGCCAGTATTCGTGGAGTCGCCTGAAATACCATTCTGGGAGACTTGTGTTCTAACCAAAAAAATGGGACAGTGTCTGGTGGGTAGT TTGACTGGGGCGGTCTCCTCCTAAAGGGTAACGGAGGAGCACGAAGGTTGGCTAATCACGGTCGGACATCGTGAGGTTAGTGTAATGGTAGAAGCCAGCT TAACTGCGAGACAGACGGTGAGCAGGTGCGAAAGGGTCATAGTGATCCGGTGGTTCTGATGGAAGGGCCATCGCTCAACGGATAAAGGTACTCTGGGATA ACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGAAGTTGGTCCAAGGGTATGCTG TTCGCCATTAAAGTGGTACGCGAGCTGGGTTCAAAACGTGTGAGACAGTTTGGTCCCTATCTGCCGTGGGCGCTGGATGTTGAAGGGATTGCTCCTAGTA CGAGAGGACCGGAGTGAACGAACGCTGGTGTATGGGTTGTCATGCCAATGCATGCCCGGTAGCTACGTCGGATCGATAACCGCTGAAACATCTAAGCGGA AGCGACCTAAGAAAGTCATCCCAGGGACGTTGGAGACTACACGTGATGGCTGG Stigmatella CTACTAAGGCGTGTGGTGGATGCCTAGGTGCCAAGGCGATGAAGGACGTGGGTGCTGCGAAAAGCTCCGGGGAGTTGCAACGAACGTGAACCGGAGATGT CCGAATGCCCACATGGGCGACCAGGGGAGTGAAACATCTCAGTACCCTGGGAAAAGAAAACAATGTGATTCCCGTAGTAGCGGCGAGCGAACCGGGAACA GCCTGGTGCTAGCGGAAGCACTTGGAAAGTGCACCAAGACGTGAAGTCGCGTAGCAAGCCCAAGTCGGCGGGACACGTGCAATCCTGCCCGAATCTGCCG GGACCATCCGGTAAGGCTAAATACTATTGGCGACCGATAGTGAAAAGTACCGCGAGGAAAGGTGAAAAGACCGGAGTCCAAAGACTGAAACCACATGTCT ACAACAGTTCGAGCGCAGCGCGAGAGGTACCTTTTGCATCATGATTCGGCGACTTAATGTACGTAGCGGGCTAAGATGGGAGCCGGAGCGAGCGGTCCGA AATGGGCGGAGTTGCGTGTATTAAACCCAAGCGGGTGATCTACACATGGCCAGATGAAGTGCGGTAACACCGCATGGAGGTCCGAACATGAAAGTTGAAA ATTTCGGGATGAGTGTTGTAGGGGTGAAAGGCCAATCAAACTCGTGATAGCTGGTCTCCCCGAAAGATATTTAGGTATCGTCTCAGGCAGTACCGAGGTA GAGCACTGGAACGGCTAGGTCCCGATAAACCGTACCAAACTCCGAATGCCGGTGCCTGGGAAGCAGTCGTGGGTGATAACGTCCATTGGCAAGAGGGGAA TAACCCAGACCGACAGCTAAGCCCCCAAACAGTCTAAGTGACAAGGATGTGCAGGTCATTGACAACCAGGAGGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAATAGCTCACTGGTCAAGACAGGCCCGAAAATGTCGGCTAAGACTAGTGCCGAAGCTTCGGGTCAGCGGTAGGGGAGCGTCCCAGTGCGGCAAGGTA GACCGAAAGGCTGCTGGAGCGACTGGGAGTGCTGATGCGAAATGAGTAGCGAAAGGGGGTGAGAAACCCCCTCGCCGTAAACCCAAGGTTCCTGGGTCAG TTAATCTTCCCAGGGTTAGCCGGAACCTAAGCTGAGGCCGAACGTAGGTGATGGAAAGCAGGTAATATTCTGCGCAGGACGGAGAGGCTAGACGACCGGG TGGCCGGCGTTCCTTCCAAGAAAAGTTCCGTACCAAACCGACACAGGTGGGTAGGAGAAAATCCTAAGGCGTTGAGAGAACTCTCCTCAAGGAACTAGGC AAATTTCCACCGTAACTTCGGAAGAAGGTGGGCCTCTAAAGTTGCAGAGAAAGGCGGAGGACTGTTTACCAAAAACACAGGCTCTGCGAAGGCGCAAGCC ACGTATAGGGTCTGACTCCTGCCCGGTGCTGGAAGGTTAAGGGGATTCGTCAAGGATGATCCGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGAGTAACGACTTCCGCGCTGTCTCGGAGAGGGACTCAGCGAAATTGAAATAGC TGTGCCGATCAGTTTACCCGCAGCAAGACGGAAGACCCCGGAACCTTTACTACAACTTGACAGTGACACTAGGGATTGACTGTGTAGGATAGGTGGGAGC CTTTGAAGCCGGGCCGCTAGGTTCGGTGGAGGCACGTGAAATACCACCCTGTTGATTTCTGTGTCTAACCATGATATTGGGACACTGTCTGGTGGGTAGT TTGACTGGGGCGGTCGCCTCCCAAAGAGTAACGGAGGCGCGCGATGGTTCCCTCAGCCCGATTGGAAACCGGGCGTCGAGTGCAATGGCATAAGGGAGCT TGACTGCGAGACAGACAGTGAGCAGGTGCGAAAGGGTCATAGTGATCCGGTGGTCCTGATGGAAGGGCCATCGCTCAACGGATAAAGGTACTCCGGGATA ACAGGCTTATCTCCCCCAAGAGTTCACATCGACGGGGAGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGGGCTGGAGCAGGTCCAAGGGTTTGCTG TTCGCCAATAAAGCGGTACGCGAGCTGGGTTCAAAACGTGTGAGACAGTTTGGTCCCTATCTGCTGTGGGCGTAGGATATTGAGAGGCCTGACCTTAGTA CGAGAGGACCGGGTTGGAGACACTCTGGTGTACCAGTTATCACGCCAGTGTACGCTGGGTAGCCAAGTTCGTTGGATAACCGCTGAAACATCTAAGCGGA AACCGCCTAAGACAGGTATCCCAGAGCCGTCGAAGACTACACGTGATGGCCGG Paracoccus CGGATAAGGCGTTTGGTGGATGCCTTGGCAGCAAGGCGATGAAGGACGTGATACCTGCGATAAGCCATGGGGAGCTGAGAAAAGCTTGATCCATGGATCT CCGAATGTTAACATAAGCGACCCGGGGACTGAAACATCTAAGTACCCGGGGAAAGGAAATCAACGATACTCCCCCAGTAGTGGCGAGCGAACGGGGACCA GCCGCCGATGACCAGAATGGCCTGGAAAGCCAGCCTAGCGGTGAAGCCCCGTAGGAGTATTAAGTGGGCGGGACACGTGAAATCCTGTCTGAAGATCGGG GGACCACCCTCGAAGGCTAAGTACTCTTGCTGACCGATAGCGAACAGTACCGTGAGGAAAGGTGAAAAGCCCGGAGTGAAAAGTCTGAAACCGGACGCCT ACAACAGTCGGAGGGGTCCCTGACGGGTACCTTTTGTATAATGGGTCAACGACTTGGTCTATCTAGCAGCTTAAGTTGGTAGGCGCAGCGAGCGGTCTTA AAAGGGCGGAGTTAGATGGATCAGACCCAAACCGATGATCTAGGCATGAGCAGCTGAAGGTTGGTAACACCAACTGGAGGGCCGAACACACCTGTTGAAA AAGGTGGGATGACTGTCCTAGGGGTGAAAGGCCAATCAAATCTGAGATAGCTGGTCTCCGCGAAAGCTATTTAGGTAGCGCGTCAGATTCTCCCGGGGTA GAGCACTGCATGGATGAGGGGCCCCTAAGTCTAAGCAAACTCCGAATACCGGAATCTGGCAGACACACGCGGGTGCTAACGTCCGTCGTGGAGAGGGAAA CAACCCTGACCAACAGCTAAGCCCCCAATCTGGCTAAGTGGAAAGCATGTGGACTTCCAAAACAACCAGGAGGTTGCTTAGAAGCAGCCTTTAAAGATAG CGTAACAGCTCACTGGTCAAGAGGTCTGCGAAGATGTCGGCTAAGCCACGAGCCGAAGCTTTGGGTTTGCGGTAGCGGAGCGTTCCGTGACTGTAAGCCG GGCCGTAAGCCCGGTGGAGTGATCGGAAGCGAGAATGTGACATGAGTAGCGAAACAGGGTGAGAGACCCTGTCGCCGAAAGTCCAAGGTTCCTGCTTAAG CTAATCTGAGCAGGGTAAGCCGGCCCCTAAGGCGAGGCCGAACGTAGTCGATGGGAACCAGGTAATATTCTGGGCGACGGATCGAGGTGTAGTTCCTCCA TCGGGAGGGCTGTTCCTGGAAATAGCACCGTACCAAACCGACACAGGTGGACGGTAGAGAATACCAAGGCGTTGAGAGAACCACATTTAAGGAACTCGGC AAAATACCTCCGTAAGTTCGCGAGAAGGAGGCCCCGCAGGGGGGCACAAACCGGGGGGGGACTGTTTACTAAAAACACAGGCTCTGCGAAGCCGTAAGGC ACGTATAGGGTCTGACGCCTGCCCGGTGCCGGAAGGTTAAAAGGAGAGGTCAAGCTTGAATTGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCCCCGCTGTCTCAAATGTGGACTCAGCGAAATTGAATTGTC TGTGAAGATCAGACTTCCCGCGGTTAGACGGAAGACCCCAGCACCTTTACTATAGCTTCGCACTGGCATCAGGATTGCGATGTGCAGGATAGGTGGTAGG CATCGAAGCGGGGACGCCAGTTCCCGTGGAGCCTCCTGAGATACCACCCTTCGCACTCTTATGTCTAACCGCGATTCCGGGACCCTGCGTGGTGGGTAGT TTGACTGGGGCGGTCGCCTCCCAAAGAGTAACGGAGGCGCGCGAAGGTTGGCTCAGAGCGGTCGGAAATCGCTCGTCGAGTGCAATGGCAGAAGCCAGCC TGACTGCAAGACTGACAGTGAGCAGAGACGAAAGGGCCATAGTGATCCGGTGGTCCCGGTGGAAGGGCCATCGCTCAACGGATAAAGGTACGCTGGGATA ACAGGCTGATGATGCCCAAGAGTCCATATCGACGGCATGTTTGGCACCTCGATGTCGGCTCATCTCATCCTGGGGCTGGAGCAGGTCCAAGGGTATGCTG TTCGCCATTAAAGAGGTACGTGAGCTGGGTTTAGAACGTGTGAGACAGTTCGGTCCCTATCTGCCGTGGGTGTAGGATATTGAGAGGATTGCCCCTAGTA CGAGAGGACCGGGGTGAACGTTCACTGGTGGACCAGTTATCGTGCCAACGTATGCTGGGTAGCTATGACGGCAGGATAAACGCTGAAGCATCTAAGCGTA AGCCCCCTAAAAAAGGTATCCCAGAGCCGTGGAAGACCACACGTGATGGCCGG Thermotoga GTACTAAGGCACGCGGTGGATGCCTTGGCGGCGAGGCGATGAAGGGCGTGGCAACTGCGATAAGCCCGGGGGAGCCGCAAGAGGCGTGATCCCGGGATTC CCGAATGGCCGAAAGTCGAACCGGGGGAGTGAAACATCTCAGTACCCCGGGAAAAGAAATCAACGAGATTCCCCTAGTAGCGGCGAGCGAACGGGGAGGA GCCCGGATCTAGCCGAACCACCTGGGAAGTGGGCCGAGAGGTGAAGCCCCGTAGCAAGCCCGAGTCCACGGGACACGTGGAATCCCGTGGGAAGCTGGGG GGACCACCCTCCAAGGCTAAATACTACCGCCGTCCGATAGCGCACAGTACCGTGAGGAAAGGTGAAAAGCCCGGAGTGAAAAGACTGAAACCGCGTGCCT ACAAAAGTCGGAGCCCTGGGTGACGGGTGCCTTTTGATTAATGAGCCCGCGAGTTGCCGTCGGTGGCGGGTTAAGCGGGTAGCCGTAGCGAGCGGTCCGA ACAGGGCGCAGTCACCGGCGGCAGACCCAAGCCGGTGAGCTACCCCTGGGCAGGTGAAGGTGGGTAAAACCCACTGGAGGCCCGAAGGTGGACAGTGAAA AGTCCCGGATGACTGGGGTAGGAGTGAAAAGCTAACCGAACCCGTGATAGCTGGTCTCCCCGAAATGCATTGAGGTGCAGCCTCGGGCTGTGCAGGGGTA GAGCACTGATGGGGCTAGGGGGTCTCGAACCCCGTCAAACTCCGAATCCCTGACCCCGGGAGTGAGCCGCGGGGGATAAGCTCCGCGGACGAGAGGGGAA CAACCCAGACCGCCGGCTAAGGCCCGAAGGTGGCTAAGTGGAAAGGATGTGAGCGCCTAAGACAGCTGGGATGTTGCTTAGAAGCAGCCTTTAAAGAGTG CGTAACAGCTCACCAGCCGAGGCGCTCCCGAAAATGTCGGCTAAGCCACCCCCCGAAGCCGCGGGTCTGCGGTAGGGGAGCTTTCCGCTAGGGTAAGGCG ACCCGCGAGGCCGCTGGACGAGGCGGAAGTGAGAATGGGGCATGAGTAGCGAAGGAGGGTGAGAATCCCTCCCCCCGTAAGCCCAAGGTACCTGGGGAAG TTCGTCCGCCCAGGGTTAGCCGGGCCCTAAGGTGAACCCGAAGGTAGCCGAAGGGAAGCCGGTAATATTCGGCGCGTGACGCAGAGGGTAGGCGCGGGGG TGGCCCTCGCTCCTGCCGAGAAAAACCCCGTTCCAAACCGACACAGGTGGGCGGCTGAGAAGGCTCAGGGGGCGGGTTAACCCTCGCCAAGGAACTCGGC AAATTGGCCCCGTAACTTCGGGAGAAGGGGTGCCGCCAGCGTCGCAGTGACAGGCCCGGGACTGTTTACCAAAAACACAGGCTCTGCTAACTCGAAAGAG AAGTATAGGGACTGACGCCTGCCCAGTGCCGGAAGGTTAAGGGGAGGGGTTTGGTCCGACCCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCATGAATGGCGTAACGACTGGGGCACTGTCTCGGCGGGGGGCCCGGCGAAATTTCAGTCTG GGTGAAGATCCCAGTACCCGCGGCTAGACGGAAGACCCCGGGAGCTTTACTGCAGCCTGGTATTGGGCTCTGGTGCATCGTGTATAGCATAGGTGGGAGG CTGTGAAGCCGCCTCGCCAGGGGCGGTGGAGCCCCATGGAATACCACCCTCGGTGCACTGAGTCCTAACCTGAAGGTGGGGACAGTGCCAGGTGGGCAGT TTGACTGGGGCGGTCACCTCCTAAAAGGTAACGGAGGTGTGCAAAGGTCGGCTCAGGTGGGTTGGAAATCCACCGCAGAGTGCAAGGGCATAAGCCGGCC TGACTGCGAGGCCGACAGCGAGCAGGGGGGAAACGGCCCTAGTGACCCGGCGGTCCCGGTGGAAGGGCCGTCGATCAACGGATAAAGTTACCCCGGGATA ACAGGCTGGTCCCGCCCGAGAGTTCACATCGACGGCGGGTTCGGCACCTCGATGTCGGCTCATCCCATCCTGGGGCTGAAGCAGGTCCAAGGGTTGGCTG TTCGCCCATAAAGGGGTACGTGAGCTGGGTTCAGACCGTGTGAGACAGGTCGGTCCCTATCTGCCGCGGGCGTAGGAGGTTGAGGGGGTCCTCCCTTGTA CGAGAGGACCGGGAGGAGGGGGCTCTGGTGTACCGGCTGTCGCGCCAGCGCACGCCGGGTAGCTACGCCCTAGCGATAACCGCTGAAACATCTAAGCGGA AGCGCCCCAAGATAGGCCTCCCAGGCCGGTCCGAGAAGAGACCTGATGGCCGG Vibrio@cholerae TGACTAAGGTACACGGTGGATGCCTGGGCAGTCAGGCGATGAAGGACGTACTAATTGCGATAAGCGCAGATAAGGCAGTAAAGCCTTGAGTCTGCGATTT CCGAATGCTGACATAGGCAACCGGGGGACTGAAACATCTAAGTACCCCGGGAGAAGAAATCAACGAGATTCCGGTAGTAGCGGCGAGCGAACCTGGATTA GCCCTAAAGTAGGTGAACAAGCTGGAAACTTGGCGTACAGGTGAAGCCCCGTACCCGCATCGAGTGGGCGGGACACGTGATATCCTGTCTGAATATGGGG GGACCATCCTCCAAGGCTAAATACTCTGACTGACCGATAGTGAACAGTACCGTGAGGAAAGGCGAAAAGACCTGAGTGAAAAGACTGAAACCGTGTACGT ACAACAGTAGGAGCACGGTGTGACTGGTACCTTTTGTATAATGGGTCAGCGACTTATATTCAGTGGCAGGTTAACTAGGGAGCCGCAGCGAGCGGTCTTA ACTGGGCGCAGTCTCTGGATATAGACCCAAACCGGTGATCTAGCCATGGGCAGTTGAAGGTTGATAACATCAACTGGAGGACCGAAGACTAATGTTGAAA AATTACGGATGACTGTGCTAGGGGTGAAAGGCCAATCAAACTCGAGATAGCTGGTCTCCCCGAAAGCTATTTAGGTAGCGCCTACGATACTACTGGGGTA GAGCACTGTTAAGGCTAGGGTTCACTAACCCTTTGCAAACTCCGAATACCAGTATCCGGGAGACACACGCGGGTGCTAACGTCCGTCGTGGAGAGGGAAA CAACCCAGACCGACAGCTAAGTCCCAAAGTTTGCTAAGTGGAAACGATGTGGAAGGCTCACACAGCTAGGATGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAATAGCTCACTAGTCGAGTCGGTCCGGAAGATGTCGGCTAAGCAATACACCGAAGCTGCGGCATTTGGGTAGGGGAGCGTTCTGTACCGTTAAGGTG AATCGTAAGTTTGCTGGAGGTATCACAAGTGCGAATGTGACATGAGTAACGAAAGGGGGTGAAAAACCTCCTCGCCGGAAGACCAAGGTTCCTGTCCAAG TTAATCGGGGCAGGGTGAGTCGACCCCTAAGGTGAGGCCGAACGTAATCGATGGGAAACGGGTAATATTCCGTACGGGACGGAGAGGCTAGGTGGCCAGA CGGCTGGCATTCCTTTCAGGAAAAGCATCGTACCAAACCGACACAGGTGGTCGGTAGAGAATACCAAGGCGTTGAGAGAACTCGGGTGAAGGAACTAGGC AAAATGGTACCGTAACTTCGGGAGAAGGTACGCTCTTCGGGTCGCAGATACCGGTGGTGAACTGTTTATTAAAAACACAGCCTGTGCAAAATCGCAAGAT ACGTATACGGTGTGACGCCTGCCCGGTGCCGGAAGGTTAATTGATGGGGTCAAGTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAATGATGGCCACGCTGTCTCCACCCGAGACTCAGTGAAATTGAAATCGC TGTGAAGATCAGTGTACCCGCGGCTAGACGGAAGACCCCGGAACCTTTACTACAGCTTGGCACTGAACATTGAACCTACATGTGTAGGATAGGTGGGAGG CTATGAAGACGTGACGCCAGTTGCGTTGGAGCCTCCTGAAATACCACCCTTGTATGTTTGTGTTCTAACTTAGATTTGAGGACAGTGCCTGGTGGGTAGT TTGACTGGGGCGGTCTCCTCCCAAAGAGTAACGGAGGAGCACGAAGGTGGGCTAATCACGGTTGGACATCGTGAGGTTAGTGCAATGGCATAAGCCCGCT TAACTGCGAGAATGACGTTGAGCAGGTGCGAAAGGGTCATAGTGATCCGGTGGTTCTGATGGAAGGGCCATCGCTCAACGGATAAAGGTACTCCGGGATA ACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGAAGTCGGTCCAAGGGTATGCTG TTCGCCATTAAAGTGGTACGCGAGCTGGGTTTAGAACGTGTGAGACAGTTCGGTCCCTATCTGCCGTGGGCGTTGGAAGTTGAAGGGGCTGCTCCTAGTA CGAGAGGACCGGAGTGGACGAACTCTGGTGTTCGGGTTGTGTCGCCAGACCATGCCCGGTAGCTAAGTCGGATTGATAAGCGCTGAAACATCTAAGCGCA AGCGACCCGAGAGAGTCTTCCCAGGGTTGTTCGAGACTAGACGTGATGGCAGG Nannocystis GTAGAAAGGCACACGGTGGATGCCTTGGCACCAAGGCGACGAAGGACGCGGCTACTGCGAAAAGCTACGGGGAACTGGAAGGAGTGTGATCCGTAGATGT CCGAATGTCCACATGAGCGACGGAGGGACTGAAACATCTAAGTACCTCCGGAGAAGAAATCAATGAGACTCCGCTAGTAGTGGCGAGCGAATGCGGATTA GCCCGGGGCTAGCAGAACGGCCTGGGAAGCCGGCCTAGAGGTGAAGCCCGGTAGCAAGCCCGAGTAGGCGGGACACGAGAAACCCTGTCTGAAGCTGGGA GGACCATCTTCCAAGGCTAAGTACTCTTGGTGACCGATAGCGTAGAGTACCGTGAGGAAAGGTGAAAAGACCTGAGTGAAAAGACTGAAACCGTGTGTTT ACAACAGTCGGAGAGCAGCTCGACGGGTACCTTTTGCATCATGAGCCAACGAGTTGTGGTCAGCGGCAGGTTAAGATGGAAGCCGAAGCGAGCAGTCTGA GAAGGGCGAAGTCGCTGGTTACAGACCCAAACTTGTGATCTATCCATGAGCAGCTGAAGCGCGGTAAGACTGCGTGGAGGGCCGAACACCACAGTTGAAA ATGTGGGGATGACTGTGATAGGAGTGAAAGGCTAATCAAACTGGAGATAGCTGGTCTCGCCGAAACATATTGAGGTATGGGGTCAGTTTGCATCGGGGTA GAGCACTGGATGGGCTAGGGACCTCTAAACCCAACCAAACTCCGAATACCGAAAGCTGGCACTCAGGCGTGAGAGCTAAGTTTCATTGCCGAGAGGGAAA GAACCCAGACCGGCAGCTAAGTCCCCAATCTCACTAAGTGGAAAGGATGTGGAGCACTCAGACAGCCAGGAGGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAACAGCTCACTGGTCGAGTGAACCCCGAAAATTCCGGCTAAGTGATGAACCGAAGCTCCGGGTAAGCGGTAGGCGAGTATTGTCTGGCGGTAATGCG TACGGAAAGAGCGTTGGAGTGCAGACAAGAGCTGATGTGGCATGAGTAGCGAAACCGGGTGAAAAACCCGGTCGCCGTAAACCCGAGGTTCCTGGGTAAG ATCATCTTCTCAGGGTTAGTCGGTCCCTAAGGCGAGGCAGAACGTAGTCGATGGGAAGCAGGGAACATTCTGCACGGGACGGAGAGGATAGCCGACGACT TGGGTCGCGGTCCTTCCAAGAAAAGCACCGTACCAAACCGACACAGGTGGGTGGGAGAACATCCCAAGGCGTTGAGAGAACTCGGGTTAAGGAACTCGGC AAATTGACACCGTAACTTCGGGAGAAGGTGTGCCCTTCGGGTTGCAGAGAATGGGGGAGGACTGTTTACCAAAAACACAGGCTCTGCGAAGTCGCAAGAC ACGTATAGGGTCTGACGCCTGCCCGGTGCCGGAAGGTTAACAGGAGATGTCAAGATCGAATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGGCGGGTAAGTTCCGTCCTGCACGAATGGCGTAACGACTTCCCCACTGTCTCGACCCGGGACTCAGCGAAATTGAAATCGG GGTGAAGATCCCCGTACCCGCGGCAAGACGGAAGACCCCGGAACCTTTACTGCAGCTTGGCACTGGTTTTCGGACTTGTCTGTGTAGGATAGGTGGGAGG CTATGATGTGGGGCCGCTAGGTTCCACGGAGCCACGTGAAATACCACCCTGAGAAGTCTGAAGCCTAACCGTGAGTCCGGGACACTGCCTGGTGGGTAGT TTGACTGGGGCGGTCACCTCCGAAAGAGTAACGGAGGCGCGCAAAGGTTCCCTCAGGCTGATTGGAAACCAGCCGAAGAGTGTAAAGGCATAAGGGAGCT TGACTGCGACTCATACAGAGAGCAGGCACGAAAGGGCCTTAGTGATCCGGTGGTTCTGATGGAAGGGCCATCGCTCAACGGATAAAGGTACTCCGGGATA ACAGGCTTATCACGCCCAAGAGTTCACATCGACGGCGTGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGGGCTGTAGTAGGTCCAAGGGTTTGCTG TTCGCCAATAAAGCGGTACGCGAGCTGGGTTCAAAACGTGTGAGACAGTTTGGTCCCTATCTGCCGTGGGCGCAGGAATTTGAGTGGACTGTCCCTAGTA CGAGAGGACCGGGATGGACAGACCCTGGTGTTCCGGTTGTTTTGCCAAGACACGCCGGGTAGCCATGTTGGACGGATAACCGCTGAAACATCTAAGCGGA AGCCACCAAAGAGAGGATTCCCAGGTCCGTCGTAGACGACACGTAATGGCCGG Rhodobacter CGGAGAAGGCGTTTGGTGGATGCCTTGGCAGCAAGGCGATGAAGGACGTGATACCTGCGATAAGTCATGGGGAGCTGAGAAAAGCTTGATCCATGAATTT CCGAATGTTTACATAGGCGACCCGGGGACTGAAACATCTAAGTACCCGGGGAAAGGAAATCAACGATACTCCGTTAGTAGTGGCGAGCGAACGCGGACCA GCCGGTGAACAGTGGAATGGTCTGGAAAGCCAGCGATATGGTGAAGCCCCGTAACAGTCATAAGTGGGCGGGACACGTGTAATCCTGTCTGAAGATCGGG GGACCACCCTCGAAGGCTAAGTACTCTTGCTGACCGATAGCGAACAGTACCGTGAGGAAAGGTGAAAAGCCCGGAGTGAAAAGTCTGAAACCGGACGCCT ACAACAGTCGGAGCTTTAAGTGACGGGTACCTTTTGTATAATGGGTCAACGACTTGGTCTTACGAGCAGCTTAAGATGGTAGGCGCAGCGAGCGGTCTTA AAAGGGCGGAGTTCGTGGGATCAGACCCAAACCGATGATCTAGCCATGTCCAGATGAAGGTTGGTAACACCAACTGGAGGTCCGAAGACACCCGTTGAAA AGGGTCGGATGAGTGTGCTAGGGGTGAAAGGCCAATCAAATCTGAGATAGCTGGTCTCCGCGAAAGCTATTTAGGTAGCGCCTCGGATACCTGCGGGGTA GAGCACTACATGGATGAGGGGCCCCTAAGTCTAAGTAAACTCCGAATACCGCTATCCGGGAGACACACGCGGGTGCTAACGTCCGTCGTGAAGAGGGAAA CAACCCTGACCAACAGCTAAGCCCCCAATCTGGCTAAGTGGAAAGCATGTGGATTTCCAAAACAACCAGGAGGTTGCTTAGAAGCAGCCTTTAAAGATAG CGTAACAGCTCACTGGTCTAGAGATCCGCGAAGATGTCGGCTAAGCCACGAGCCGAAGCTTTGGATAAGTGGTAGCGGAGCGTTCTGTGACTGTAAGCCG GCCTGTGAGGCCGGTGGAGTGATCAGAAGCGAGAATGTGACATGAGTAGCGAAAGAGGGTGAGAGACCCTCTCGCCGAAAGTCCAAGGTTCCTGCTTAAG CTAATCTGAGCAGGGTAAGCCGGCCCCTAAGGCGAGGCCGAACGTAGTCGATGGGAACCACGTAATATTGTGGGCGTGACGGATGCTCACGTTGTCGACA TCGGTCGCAGCTGTCCCAGGAAATACACCGTACCAAACCGACACAGGTGGACGGTAGAGTATACCAAGGCGTTGAGAGAACCACGTTTAAGGAACTCGGC AAAATGCCTCCGTAAGTTCGCGAGAAGGAGGCCCCACAGGGGGGGACAAACTGGGGGGGGACTGTTTACTTAAAACACAGGCTCTGCGAAGCCGTAAGGC ACGTATAGGGTCTGACGCCTGCCCGGTGCTGGAAGGTTAAAAGGAGGGGTCAAGTCCGAATTGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGATCTCCCCGCTGTCTCAAACGTGGACTCAGCGAAATTGAACTGTG TGTCAAGATCACACTACCCGCGGTTAGACGGAAGACCCCAGAACCTTTACTCCAGCTTTGCACTGGCATCAGGATTGTGATGTGCAGGATAGGTGGTAGC CTTTGAAACCGTGACGCCAGTTGCGGTGGAGGCCCCTGAGATACCACCCTTCGCACTCTTATGTCTAACCGCGATTCCGGGACCCTGCATGGTGGGGAGT TTGACTGGGGCGGTCGCCTCCCAAATCGTAACGGAGGCGCGCGAAGGTAGGCTCAGACCGGTCGGAAATCGGTCGTTGAGTGCAATGGCAAAAGCCTGCC TGACTGCAAGACTGACAGTGAGCAGAGACGAAAGGGTCATAGTGATCCGGTGGTCCCAGTGGGAGGGCCATCGCTCAACGGATAAAGGTACTCTGGGATA ACAGGCTGATGATGCCCAAGAGTCCATATCGACGGCATGTTTGGCACCTCGATGTCGGCTCATCTCATCCTGGGGCTGGAGCAGGTCCAAGGGTATGCTG TTCGCCATTAAAGAGGTACGTGAGCTGGGTTTAGAACGTGTGAGACAGTTCGGTCCCTATCTGCCGTGGGTGTAGGATATTGAGAGGATTGCCCCTAGTA CGAGAGGACCGGGGTGAACGTTCACTGGTGGACCAGTTATCGTGCCAACGTATGCTGGGTAGCTATGACGGCAGGATAAACGCTGAAGCATCTAAGCGTA AGCCCCCTAAAACAGGTATCCCAGGGCCGTGGAAGACCACACGTGATGGCCGG Streptomyces@coelico TTTTTAAGGCGCACGGTGGATGCCTTGGCACCAAACCGATGAAGGACGTGGGAGCCACGATAGGCCCCGGGGAGTCGCAACAGGCTTGATCCGGGGGTGT CCGAATGCCCACATGGGGGACGCGGGGAGTGAAACATCTCAGTACCCGCGGAAGAGAAAACAACGTGATTCCGGGAGTAGTGGCGAGCGAAACCGGATGA GGCCGGATGTAGGCGAAGACATGCGAAAGTCCGGCTAGAGGTAAACCCCCGTATCAACCCCAAGTGCACGGGGCCCGAGAAATCCCGTGTGAATCTGGCG GGACCACCCGCTAAGCCTAAATATTCCTGGTGACCGATAGCGGATAGTACCGTGAGGAATGGTGAAAAGTGCGGAGTGAAAAGACTGAAACCGTGTGCCT ACAACCGTGGGAGCGTTTCGTGACTGGTGCCTTTTGAAGAATGAGCCTGCGAGTTTGGGTGTGTTGCGGGTTAACAGGGAAGCCGTAGCGAGCGGTCCGA ATAGGGCGTAGTAGCACGCTCAAGACCCAAGCGAGTGATCTAGCCATGGGCAGTTGAAGCGGCTTAAGAGGTCGTGGAGGACCGAACACCAGGGTTGAAA ACCTGGGGATGACTGTGTTAGGGGTGAAAGGCCAATCAAACTCGTGATAGCTGGTCTCCCCGAAATGCATTTAGGTGCAGCGTCGTGTTCTGCCGAGGTA GAGCACTGGATAGGCGAGGCCTCGGTAACCTTAGCCAAACTCCGAATGCCGGAGCGCGGCAGTGAGACGTGGGGGATAAGCTCCATGGTCGAGAGGGAAA CAGCCCAGAGCATCGACTAAGCCCCTAAGGACGCTAAGTGGAAAGGATGTGAGTCGCACAGACAACCAGGAGGTTGCTTAGAAGCAGCCTTGAAAGAGTG CGTAATAGCTCACTGGTCTAGTGATTCCCGACAATGTCGGCTAAGCGTACCGCCGAAGTCGTGTCAAATGGGTAGGGGAGCGTCGTGTGCGGGTAAGCAG CCGCGGAACGGTTGTGGACGGTTCACGAGTGAGAATGAGGCATGAGTAGCGAACAAACGTGAGAAACGTTTGCGCCGATTGACTAAGGTTCCTGGGTCAG CTGATCTGCCCAGGGTAAGTCGGGACCTAAGGCGAGGCCGAACGTAGTCGATGGATAACCGGTGATATTCGGTACGTGACGCAGAAGGTAGTCCACCCGG TGGCGGGGGATTCTGTCGAGAAAAGCCCCGTACCAAACCGACTCAGGTGGTCGGTAGAGAATACCGAGGCGTCGGGTGAACTATGGTTAAGGAACTCGGC AAAATGCCCCCGTAACTTCGGGAGAAGGGGGGCCACTTGTGCCGCAGAGACCGCGAGAGGACTGTTTACTAAAAACACAGGCCGTGCGAAGCCGTAAGGC ATGTATACGGACTGACGCCTGCCCGGTGCTGGAACGTTAAGGGGACCGGTTCGGTGAGAACTTAAGCGCCAGTAAACGGCGGTGGTAACTATAACCATCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCTCGACTGTCTCAACCATAGGCCCGGTGAAATTGCACTACG AGTAAAGATCTCGTTTCGCGCAGCAGGACGGAAGACCCCGGGACCTTTACTACAGTTTGATATTGGTGTTCGGTTCGGCTTGTGTAGGATAGCTGGGAGA CTTTGAAGCTCGCACGCCAGTGTGGGTGGAGTCTCGTGAAATACCAGTCTGGTCGTGCTGATGTCTAACCTGGATTCAGGGACAGTGTCTGATGGGTAGT TTAACTGGGGCGGTTGCCTCCTAAAGAGTAACGGAGGCGCCCAAAGGTTCCCTCAGCCTGGTTGGCAATCAGGTGTTGAGTGTAAGTGCACAAGGGAGCT TGACTGTGAGACCGACGGTGAGCAGGGACGAAAGGGGACTAGTGATCCGGCGGTGGCTGTGGAAGCGCCGTCGCTCAACGGATAAAGGTACCCCGGGATA ACAGGCTGATCTTCCCCAAGAGTCCATATCGACGGGATGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGTCGGTCCAAGGGTTGGCTG TTCGCCCATAAAGCGGTACGCGAGCTGGGTTTAGAACGTGTGAGACAGTTCGGTCCCTATCCGCTGTGCGCGTAGGAGTTTGAGAAGGCTGTCCCTAGTA CGAGAGGACCGGGACGGACGAACTCTGGTGTGCCAGTTGTCCTGCCAAGGCAGGCTGGTTGGCTACGTCGGAGGGATAACCGCTGAAACATCTAAGCGGA AGCCTCTTGAGAGAGGACTCCCAGGCTCCCAGTAGACGACGGGTGATGGCCGG Campylobacter@jejuni CTACTAAGGCGAATGGTGGATGCCTTGACTGGTAGGCGATGAAGGACGTACTAGCTGCGATAAGCTACGGGGAGCTGTCAAAAGCTTGATCCGTAGATTT CCGAATGCCTATATGGGCGACGAGGGGATTGAAACATCTTAGTACCCTCGGAAAAGAAATCAATGAGATTGCGTCAGTAGCGGCGAGCGAAAGCGCAAGA GGGCGGATTTAGCAGAACATTCTGGAAATATAGCCTAGAGGTGAAGTCCCGTAGCAAACCTGAGTGGGCGGGACACGAGGAATCCTGTCTGAATCCGGGT CGACCACGATCCAACCCTAAATACTATACCAGATCGATAGTGCAAAGTACCGTGAGGAAAGGTGAAAAGAGAGAAGTGAAAAGACTGAAACCATTTGCTT ACAACATTCAGAGCACCGTGTGATGGCTGCCTTTTGCATAATGAGCCTGCGAGTTGTGGTGTCTGGCAGGTTAAGAAGGAAGCCGTAGCGAGCGGTCTGA ATAGGGCGTAGTCAGATGCTGCAGACCCAAACGAGTGATCTATCCATGAGCAGTTGAAGCTAGTTAAGAACTAGTGGAGGACTGAACATAGGCGTTGAAA AGCCCGGGATGACTGTGATAGGGGTGAAAGGCCAATCAAACTTGTGATAGCTGGTCTCTCCGAAATATATTTAGGTATAGCGTTGTGAATATAAGGGGTA GAGCACTGAATGGGCTAGCATCCATGAAACCCTATCAAACTCCGAATACCTTTGCACAGCAGTCAGGCGCGAGTGATAAAATCCGTCGTCAAGAGGGAAA CAACCCAGACTACCAGCTAAGTCCCTAAACTACTTAAGTGGAAACGATGTAAGTTACTTAAACAACCAGGAGGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAATAGCTCACTGGTCTAGTGATTTCGGAAAATATCGGCTAAAGTAAGTACCGAAGCTGTAGACTTGTGGTAGGAGAGCGTTCTATTGCGTCAAGGTA TACCGTAAGAGTGCTGGAGCGAATAGAAGTGAGCATGAGGCATGAGTAGCGAATTAATGTGAGAATCATTAACGCCGTAAACCCAAGGTTCCTACGCGAG CTCGTCATCGTAGGGTTAGTCGGGTCCTAAGTCGAGTCCGAAGGTAGACGATGGCAAATTGGTAATATTCAATACAGGACGCTTGGGCTAAGGGGCTAGA TGGCTAGCCCTCGAGCCAAGAAAAGTCCCGTACCAAACCGACACAGGTGGGTGGGAGAGTATTCTAAGGCGGTGGAAGAACTCTCTTTAAGGAACTCTGC AAAATAGCACCGTATCTTCGGTATAAGGTGTGGTTATAAACTTACAACAAAGGTCCCCCGACTGTTTACCAAAAACACAGCCTCTGCTAACTCGTAAGAG ATGTATAGGGTGTGACGCCTGCCCGGTGCTCGAAGGTTAATTGATGGGGTTTAGTCTTGATCGAAGCCCGAGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGTTAAATACCGACCTGCATGAATGGCGTAACGAGATGGGAGCTGTCTCAAAGAGGGATCCAGTGAAATTGTAGTGGA GGTGAAAATCCTCCTACCCGCGGCAAGACGGAAGACCCCGGGACCTTTACTACAGCTTGACACTGCTACTTGGATAAGAATGTGCAGGATAGGTGGGAGG CTTTGAGTATATGACGCCAGTTGTATATGAGCCTTGTGAGATACCACTCTTTCTTATTTGGTAGCTAACCAGCATAGTGGGACAATGTCTGGTGGGTAGT TTGACTGGGGCGGTCGCCTCCCAAATAATAACGGAGGCTTACAAAGGTTGGCTCAGAACGGTTGGAAATCGTTCGTAGAGTATAAAGGTATAAGCCAGCT TAACTGCAAGACATACAGTAAGCAGAGACGAAAGGGTCTTAGTGATCCGGTGGTTCTGGTGGAAGGGCCATCGCTCAAAGGATAAAGGTACCCCGGGATA ACAGGCTGATCTCCCCCAAGAGCTCACATCGACGGGGAGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGGGCTGGAGCAGGTCCAAGGGTATGCTG TTCGCCATTAAAGCGGTACGCGAGCTGGGTTCAGAACGTGTGAGACAGTTCGGTCCCTATCTGCCGTGGGCGTAAGAAGTTGAAGAGATTGACCCTAGTA CGAGAGGACCGGGTTGAACAAACACTGGTGTAGCTGTTGTTCTGCCAAGACACGCAGCGTAGCTAAGTTGGAAGGATAAACGCTGAAACATCTAAGCGTA AGCCACTCAAGAGAATCTTCTCAGCTCTCTAGAAGACTACAGTTGATGGCTGG Rhodobacter@sphaeroi CGGAAAAGGCGTTTGGTGGATGCCTAGGCAGCAAGGCGATGAAGGACGTGATACCTGCGTTAAGCCATGGGGAGCCGGGAAGGGCTTGATCCATGGATGT CCGAATGCTTACATGAGCGACCCGGGGACTGAAACATCTAAGTACCCGGGGAAAGGAAATCAACGAGACTCCGCTAGTAGTGGCGAGCGAACGCGGACCA GCCGCTCAGTACTGGAATGGCCTGGAAAGCCAGCCCAGCGGTGAAGCCCCGTAAGAGCTATAAGTGGGCGGGACACGTGAAATCCTGTCTGAAGATCGGG GGACCACCCCCGAAGGCTAAGTACTCTTGCTGACCGATAGCGAACAGTACCGTGAGGAAAGGTGAAAAGCCCGGAGTGAAAAGACTGAAACCGGACGCCT ACAACAGTCGGAGGGTTACCTGACGGGTACCTTTTGTATAATGGGTCAACGACTTGGTCTCACGAGCAGCTTAAGGTGGGAGGCGCAGCGAGCGGTCTTA AAAGGGCGGAGTTCGTGGGATCAGACCCAAACCGGTGATCTAGCCATGAGCAGATGAAGTCAGGTAACACCTGATGGAGGTCCGAAAACACCCGTTGAAA AGGGTTGGATGACTGTGCTAGGGGTGAAAGGCCAATCAAACCTGAGATAGCTGGTCTCCGCGAAAGCTATTTAGGTAGCGCCTCGGATACCTCGGGGGTA GAGCACTGCATGGATGAGGGGCCCCTAAGTCTAAGCAAACTCCGAATACCCGTATCCGGGAGACACACGCGGGTGCTAACGTCCGTCGTGAAGAGGGAAA CAACCCTGACCTGCAGCTAAGCCCCCAATCTGGCTAAGTGGAAAGCATGTGGACGGCCAAAACAACCAGGAGGTTGCTTAGAAGCAGCCTTTAAAGATAG CGTAACAGCTCACTGGTCTAGCTGTCCGCGAAGATGTCGGCTAAGCCACGAGCCGAAGCTCAGGATCAGTGGTAGCGGAGCGTTCCGTGTCTGTAAGCCG GGCCGTAAGCCCGGTGGAGAGATCGGAAGCGAGAATGTGACATGAGTAGCGAAACAGGGTGAGAGACCCTGTCGCCGAAAGTCCAAGGTTCCTGCTTAAG CTAATCTGAGCAGGGTAAGCCGGCCCCTAAGGCGAGGCCGAACGTAGTCGATGGGAACCAGGTAATATTCTGGGCGTGACGGATCGCAGGGTAGTCGGTA TCGACCGCTGCGGTCCCTGGAAATACACCGTACCAAACCGACACAGGTGGACGGTAGAGAATACCAAGGCGTTGAGAGAACCACATCAAAGGAACTCGGC AAAATGCCTCCGTAAGTTCGCGAGAAGGAGGCCCCGCAGGGGGGCACAAACCGGGGGGGGACTGTTTACTTAAAACACAGGCTGTGCGAAGCCGCAAGGC ACGTATACAGTCTGACGCCTGCCCGGTGCTGGAAGGTTAAAAGGAGGAGTCAAGTCCGAATTGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGATCTCCCCGCTGTCTCTGATGTGGACTCAGCGAAATTGAACTGTG TGTCAAGATCACACTTCCCGCGGTTAGACGGAAGACCCCAGAACCTTTACTATAGCTTCGCACTGGCATCAGGATTGTGATGTGCAGGATAGGTGGTAGG CATCGAAGCGGGGACGCCAGTTCCCGTGGAGCCACCTGAGATACCACCCTTCGCCATCTTATGTCTAACCGCGATTCCGGGACCCTGCGTGGTGGGTAGT TTGACTGGGGCGGTCGCCTCCCAAACAGTAACGGAGGCGCGCGATGGTGGGCTCAGACCGGTCGGAAATCGGTCGTCGAGTGCAATGGCAGAAGCCCGCC TGACTGCAAGACTGACAGTGAGCAGAGACGAAAGGGCCATAGTGATCCGGTGGTCCCGGTGGAAGGGCCATCGCTCAACGGATAAAGGTACTCTGGGATA ACAGGCTGATGATGCCCAAGAGTCCATATCGACGGCATGTTTGGCACCTCGATGTCGGCTCATCTCATCCTGGGGCTGGAGCAGGTCCAAGGGTATGCTG TTCGCCATTAAAGAGGTACGTGAGCTGGGTTTAGAACGTGTGAGACAGTTCGGTCCCTATCTGCCGTGGGTGTAGGAGATTGAGAAGATTGCCCCTAGTA CGAGAGGACCGGGGTGAACGATCACTGGTGGACCAGTTGTCGTGCCAACGCATGCTGGGTAGCTATGACGGCAGGATAACCGCTGAAGCATCTAAGCGGA AGCCCCTTAAAAAAGGTCTCCCAGGGCCGTGGAAGACCACACGTGATGGCCAG Zymomonas TGGGTAAGGCATTTGGTGGATGCCTAGGCATACAGGCGATGAAGGACGTGGCACCTGCGATAAGCTACGGCGAGATGTGAGAATCTTGACCCGTAGATTT CCGAATGTACACATGAGCGACCCGGCGACTGAAACATCTAAGTACCCGGGGAAAAGACATCAACGAGATTCCGTTAGTAGTGGCGAGCGAACGCGGAGTA GGCCCCTGTTAGCAGAAGTCTTTGGAAAAGACACCTAGTGGTGAAGTCCCGTAGTAAATCTGAGTGGGCGGGGCACGTGAAACCTTGTCTGAACATGGGG GGACCACCCTCCAAGCCTAAATACTCTGTATGACCGATAGTGAAAAGTACCGTGAGGAAAGGTGAAAAGACCGGAGTGAAAAGTCTGAAACCGAATGCTT ACAACAGTAGGAGGGTAGCCTGACTGGTACCTCTTGCATAATGGGTCTGTGACTTAATGTATCAAGCAGCTTAAGATGGTAGGCGCAGCAAGCGGTCTGA ATAGGGCGTAGTTTGATGCATTAGACCCAAACCGGCGATCTAGGCATGGTCAGATGAAGGTAAGTAACACTTACTGGAGGTCCGAAGATTAACGTTGAAA AGTTACGGATGAATGTTTTAGGGGTGAAAGGCCAATCAAGCCGGAAATAGCTGGTCTCCGCGAAAACTATTGAGGTAGTGCCTCATGGACCGTTGGGGTA GAGCACTGGATGGATGCGGGTCGACCAAATCTAACCAAACTCCGAATACCAATTCATGGGAGACAGACGCGGGTGCTAAGGTCCGTCGTCGAGAGGGAAA CAGCCCTGACCTACAGCTAAGTCCCCAAGCTGTCTAAGTGGAAAGCTTGTAAGACCCCAAAACAACCAGGAGGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAACAGCTCACTGGTCTAGGGTCTTGCGAAGATGTCGGCTAAGACATGCACCGAAGCTTAGGATTTATGGTAGCGGAGCGTTCCGTACCTGTAAGCAG TCTGGTAAGGACTGTGGAGGTATCGGAAGTGCGAATGAGACATGAGTAGCGAAATAGGGTGAGATGCCCTATCGCCGAAAGTCCAAGGTTCCTGCGCAAG CTAATCCGCGCAGGGTGAGTCGGCCCCTAAGACGAGCCCGAAGGTAGTCGATGGGAAACAGGTAATATTCTGTACGTGACGGATCGTGTAATTGTTGTCA TCGGACACTCAGGTTCCAGGAAATACACCGTACCAAACCGACACAGGTGGACGGTAGAGTATACCAAGGCGTTGAGAGAAGGGTGTTGAAGGAACTCGGC AAATTGCCTCCGTACCTTCGGAAGAAGGAGGCCCTTCATAGGGGCACAGGCCGGGGGAGGACTGTTTAGCAAAAACACAGGCTCTGCAAAGTCGCAAGAC ACGTATAGGGCCTGACGCCTGCCCGGTGCTGGAAGGTTAAGTGGAGGAGTCAAGTCTGAAATGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCCCCACTGTCTCCAACACCTGCTCAGCGAAATTGAATTCTC CGTGAAGATCGGAGTACCCGCGGTTAGACGGAAGACCCCGGCACCTTTACTGCAGCTTCAGAGTGGCATTAGGAAAGAACTGTGTAGCATAGGTGGGAGG CTTTGAAACTTGAGCGCCAGCTTGAGTGGAGCCTAGTGAAATACCACCCTGTTGTTTTCTATGTCTAACCTAGAATCAGGGACCCTCTGTGGCGGGTAGT TTGACTGGGGCGGTCGCCTCCTAAAGAGTAACGGAGGCGCGCGATGGTTGGCTCAGGCCGGTTGGAAACCGGCTCAAGAGTGCAATGGCATAAGCCAGCC TGACTGTGAGACTGACAGTGAACAGAGACGAAAGGGTCATAGTGATCCGGTGGTCCCTGTGGAAGGGCCATCGCTCAACGGATAAAGGTACGCCGGGATA ACAGGCTGATAACCCCCAAGAGCTCATATCGACGGGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGGAGCAGGTCCAAGGGTTTGCTG TTCGCCAATAAAGTGGTACGTGAGCTGGGTTCAGAACGTGCGAGACAGTTTGGTCCCTATCTGCCGTGGGCGTCGATATTTGAGAGGATTGCCCTTAGTA CGAAAGGACCGGGGTGAACATGCTCTGGTGGACCTGTCGTGGCGCCAGCCCGAGCAGGGTAGCTATGCTGGCGGGATAACCGCTGAAACATCTAAGCGGA AGCCTCCTAAGATAAGATATCTAGAGCCGTCGAAGACTACACGTGATGGCCAG Brevundimonas CGTTGAAGGCTTCTGACGGATGCCTTGGCGTAGAGGCGATGAAAGACGTGGCAACTGCGATAAGAACCGGGGAGGCGCTAGACCCTTGATCCGGTTATCT CTGAATGCAAACATTGGCGACCCGGGGACTGAAACATCTCAGTACCCGGGGAAAGGACATCAACGAGACTCCCGTAGTAGTGGCGAGCGAACCGGGACCA GGCCTCTTAAAGTCGAACGGAATGGAAATCCGGCCTAGCGGTGAAGCCCCGTAACCAAACTGAGTGGGCGGGACACGTGAAATCCTGTCTGAACATGGGG GGACCACCCTCCAAGCCTAAGTACTCTCTACGACCGATAGTGAAAAGTACCGTGAGGAAAGGTGAAAAGCCCGGAGTGAAAAGTCTGAAATCGGAAGCCT ACAACAGTCGGAGCCGACGGTGACGGGTACCTTTTGTATAATGGGTCAGCGACTTCATGTGTCGAGCAGCTTAAGTTGGTAGGCGCAGCGAGCGGTCTGA ATAGGGCGAAGTTCGACGTATGAGACCCAAACCGGTGATCTATCCATGAGCAGATGAAGGTAAGTAACACTTACTGGAGGTCCGAACGTGAATGTTGAAA AATTCGGGATGACTGTGATAGGGGTGAAAGGCCAATCAAACCTGACATAGCTGGTCTCCGCGAAATCTATTTAGGTAGAGCGTCCGATACCCTGGGGGTA GAGCACTGGATGGTTGCGCTGCACGGAATACTAACCAAACTCCGAATACCCATATCGGGCAGACACACGCGGGTGCTAACGTCCGTCGTGAAAAGGGAAA CAACCCTAACCATCATCTAAGCCCCCAAGCTGGCTAAGTGGAAACGATGTGGATTGCTTTGACAATCAGGAGGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAACAGCTCACTGATCAAGCGATCCCGGAAAATGTCGGCTAAGCCATGCGCCGAAGATATGGGTTTGCGGTAGCGGAGCGTTCCGTACCTGTAAGGTC AACTGTGAGTTGGCTGGAGGTATCGGAAGTGAGAATGTGACATGAGTAACGAAACAGTGTGAGAAACACTGTCGCCGAAAGACCAAGGTTCCTGCGTAAG CTAATCTGCGCAGGGTTAGTCGGCCCCTAAGGCGAGGCTGAACGTAGTCGATGGGAAGCAGGTAATATTCTGCACGTGACGGATGGCATAGTCGTGGGGA TTGTTCCCGGTTGTCCCTGGAAATACACCGTACCAAACCGACACAGGTGGTCGGTAGAGTATACCAAGGCGTTGAGAGAACTGTGCTGAAGGAACTCGGC AAATTGCACGCGTAACTTCGGAATAAGCGTGACTCACACGGTGGCACAAGCCGGGGGAGGACTGTTTAGCAAAAACATAGGCTCTGCGAAGCATCAATGC ACGTATAGGGTCTGACGCCTGCCCGGTGCCTGAAGGTTAAAGGGAGGAGTAAAGTCCGAACTGAAGCCCAGGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCCCCACTGTCTCCAGCACAGGCTCAGTGAAATTGAATTCCC CGTGAAGATCGGGGTTCCCGCGGTCAGACGGAAGACCCTAGAACCTTTACTATAGCTTCGCCTTGGCGTTAGCGACCGTATGTGTAGGATAGGTGGGAGG CTATGAAGCCGGGGCGCCAGCTCTGGTGGAGCCTCCTGAAATACCACCCTTACTGTCGTTACGTCTAACCGAGATCCCGGGACATGGCGTGGTGGGTAGT TTGACTGGGGCGGTCGCCTCCCAAAGTGTAACGGAGGCGCGCGATGGTTAGCTCAGACCGGTCGGAAATCGGTCGTCGAGTGCAATGGCATAAGCTAGCC TGACTGCGAGACTGACAGTGAGCAGAGACGAAAGGGCCATAGTGATCCGGTGGTCCCGGTGGAAGGGCCATCGCTCAACGGATAAAGGTACTCTAGGATA ACAGGCTGATTTTGCCCAAGAGTCCATATCGACGGCAAGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGGAGCAGGTCCAAGGGTATGCTG TTCGCCATTAAAGTGGTACGTGAGCTGGGTTCAGAACGTGTGAGACAGTTTGGTCCCTATCTGCCGTGGGTGTTCGAAGTTGAGAGGACTGTCCCTAGTA CGAGAGGACCGGGATGGACATACTCTGGTGGACCTGTCATGGCGCCAGCCTGAGCAGGGTAGCTAAGTTGGATAGATAACCGCTGAAACATCTAAGCGGA AACTACCTAAAAAAGGCTTCGCAGGATCGTGGAAGACTACACGTGATGGCCAG Listeria@monocytogen TTAGAAAGGCGCACGGTGGATGCCTTGGCACTAAGCCGAAGAAGGACGGGACTACACCGATATGCTTTGGGGAGCTGTACGAAGCGTGATCCAGAGATTT CCGAATGTCCACATGAGCAACCCAGGGACTGAAACATCTAAGTACCTGGGGAAGAGAAAGAAAATCGATTTCCTGAGTAGCGGCGAGCGAAACGGAAAGA GCCCGGATATAAATGAAGGGTCTGGAAAGCCCGCCAAGAGGTAAAGCCCGGTATTAATCCTGAGTCGGCGGAACACGTGAAATTCCGTCGGAATCCGGGA GGACCATCTCCCAAGGCTAAATACTCCTAGTGACCGATAGTGAACAGTACCGTGAGGAAAGGTGAAAAGCCCGGAGTGAAAAGTCTGAAACCGTGTGCCT ACAATAGTTAGAGCCCAGGGTGATAGGTGCCTTTTGTAGAATGAACCGGCGAGTTACGATTTGTTGCAGGTTAAGAAGGGAGCCGTAGCGAGCGGTCTGA ATAGGGCGAAGTAACAGGTCGTAGACCCAAACCGGTGATCTACCCATGTCCAGATGAAGGTAAGTAATACTTACTGGAGGTCCGAACACGCACGTTGAAA AGTGCGGGATGAGTGTGGTAGCGGAGAAATTCCAATCGAACTTGAGATAGCTGGTCTCTCCGAAATAGCTTTAGGGCTAGCCTCGAGGAGTCATGAGGTA GAGCACTGTTTGGACTAGGCCTTGGTAAATTCAGATAAACTCCGAATGCCATTTCTCGGGAGTCAGACGCGAGTGATAAGATCCGTAGTCGAAAGGGAAA CAGCCCAGACCACCAGTTAAGTCCCCAAAAATGTTAAGTGGAAAGGATGTGGGTTGCTTAGACAACCAGGATGTTGCTTAGAAGCAGCCTTGAAAGAGTG CGTAATAGCTCACTGGTCGAGTGACCCCCGAAAATGTCGGCTAAACATATTACCGAAACTGTGGATTTGTGGTAGGAGAGCGTTCTAAGGCGGTAAGTCA GACCGGAAGACTGGTGGAGCGCTTAGAAGTGAGAATGCGGTATGAGTAGCGAAGAAGGGTGAGAATCCCTTCCACCGAATATCTAAGGTTCCTGAGGAAG CTCGTCCGCTCAGGGTTAGTCGGGACCTAAGCCGAGGCCGAACGTAGGCGATGGACAACAGGTGAGATTCTGTACGTGACACAGAGGATAGGGAACGCAA TGGTGCGTCCTCCTGTCAAGAAAAGCCCCGTACCAAACCGACACAGGTAGATAGGAGAGAATCCTAAGGTGGCGAGAGAACTCTCGTTAAGGAACTCGGC AAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCTCAGGGCCGCAGTGAATGGCCCAGGACTGTTTAGCAAAAACACAGGCTCTGCAAAACCGTAAGGT ACGTATAGGGGCTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGAGTGCTTCGGTACGAATTGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCCGCACGAAAGGCGCAACGATCTGGGCACTGTCTCAACGAGAGACTCGGTGAAATTATAGTACC TGTGAAGATCAGGTTACCCGCGACAGGACGGAAGACCCCGGGAGCTTTACTGCAACCTGATATGGAATGTTTGTACCGCTTGTACAGGATAGGTAGGAGC CGAAGAGACGTGTGCGCTAGCATACGAGGAGGCATGTGGGATACTACCCTGGCTGTATGACATTCTAACCCGCAGGGGGAGACAGTGTCAGGTGGGCAGT TTGACTGGGGCGGTCGCCTCCTAAAGAGTAACGGAGGCGCCCAAAGGTTCCCTCAGAATGGATGGAAATCATTCGCAGAGTGTAAAGGCACAAGGGAGCT TGACTGCGAGACTGACAGTGAGCAGGGACGAAAGGGGCTTAGTGATCCGGTGGTTCCGATGGAAGGGCCATCGCTCAACGGATAAAGCTACCCCGGGATA ACAGGCTTATCTCCCCCAAGAGTCCACATCGACGGGGAGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGTAGTCGGTCCAAGGGTTGGCTG TTCGCCCATAAAGCGGCACGCGAGCTGGGTTCAGAACGTGTGAGACAGTTCGGTCCCTATCCGTCGCGGGCGCAGGAAATTGAGAGGACTGTCCTTAGTA CGAGAGGACCGGGATGGACACACGCTGGTGTACCAGTTGTTCCGCCAGGACACGCTGGGTAGCTATGTTGGAGGGATAAACGCTGAAACATCTAAGCGTA AGCCCCCTAAGAGAGATTTCCCAGATCCCTGAAAGATGATAGGTGATGGTTTG Erysipelothrix@rhusi TATGTAAGGCGTACGGTGGATGCCTAGGCACTAAGCTGATGAAGGACGCGATAACAGCGAAATGCCTCGGGGAGTGGTACGACACAAGATCCGGGGGTAT CCGAATGCACACATTGGCAACCTTGTGATTGAAACATCTTAGTAACAAGGGAAAAGAAAACAAAGTGATTCCCTGAGTAGTGGCGAGCGAAACGGGAAGA GCCCGGAGTTAGTCGAATGGCATTGAAAGCCAGTCAAGAGGTGCAACCCTGTAACAAGCCTGAGTCGGCGAGGCACGAGAAACCTTGTCGGAACCAGCCG GGACCACCCGGTAAGGCTAAATACTCTTAGTGACCGATAGTGAACAGTACCGTGAGGAAAGGTGAAAAGAGCGGAGTGAAAAGACTGAAACCGTATGCTT ACAAAAGTCAGAGCCCAGGGTGATGGGTGCCTTTTGTAGAATGAACCGGCGAGTTACCATAATGTGCGGGTTAAGAAAGGAGCCGTAGCGAGCGGTCTGA ATAGGGCGTAGTACATTGTGGTAGACCCAAACAAGTGATCTAGCCATGACCAGTTGAAGTTTGGTGAAACCAAATGGAGGACCGAAGACTGTCGTTGAAA AGCCACGGATGAGTGTGCTAGCGGAGAAATTCCAATCGAACTTGATATAGCTGGTCTCCCCGAAATAGCTTTAGGGCTAGCGTCAATAGGCACTGAGGTA GAGCACTGAATGTATGAGCCCTTGGGAAATATAATCAAACTCCGAATGCCAGTGGTTGGCAGTCAGACGTGGGTGATAAGGTCCATAGTCGAAAGGGAAA CAGCCCAGATCGCCAGTTAAGTCCCAAAATATACTAAGTGGAAAGGATGTGGGATGCACAGACAACTAGGAGGTTGCTCAGAAGCAGCCTTTAAAGAGTG CGTAACAGCTCACTAGTCGAGTGACCCCCGAAAATTTCGGCTAAGTATGATACCGAAACTGCGGATAAGTGGTAGGGGAGCGTTCTATAGCGTTAAGATG TACCGTAAGAGCGTTGGAGCGTATAGAAGTGAGAATGCGGTGTGAGTAGCGAATGTCAGTGAGAATCTGACACACCGATTGCCTAAGGTTCCAGGGGAAG CTCGTCCTCCCTGGGTAAGTCGGGACCTAAGATGAGGCTGAACGTAGTCGATGGACAACAGGTGATATTCTGTACATGACAGAGAGGCTAAGTTTCCAGC TGGCTGGAACCCCTCTCAAGAAAAGTCCCGTACCAAACCGACACAGGTAGGCAGGAGAGAATCCTGAGGTGGCGAGAGAACTGTTGCCAAGGAACTCGGC AAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCTAAGGGCCGCAGTGAAGGGCCCAAGACTGTTTAACTAAAACATAGCCTCTGCGAAGTCGCAAGAC AAGTATAGGGGGTGACGCCTGCCCGGTGCTGGAAGGTTAAGGGGATGTGTTCGGATTGAACTGAAGCCCCAGTGAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCCGCACGAAAGGCGTAACGATTTGGGCGCTGTCTCGGCAGCAGACTCGGTGAAATCTTAGTACC GGTAAAGATCCGGTTACCCGCAACTAGACGGAAGACCCCAGGAGCTTTACTGTAGCTTGATATTGAATTTTGATCCTACATGTACAGGATAGGTGGGAGA CAATGAAGCATGCACGCTAGTGTATGTGGAGTCCCATGGGATACCACTCTTGTATGTTTGAATTCTAACCGCGATACCGGGAGAGTGTCAGGTGGGCAGT TTGACTGGGGCGGTCGCCTCCTAAAGAGTAACGGAGGCGCCCAAAGGTACCCTCAGATTGGTTGGAAATCAATCGACGAGCGTAAAGGCAGAAGGGTGCT TGACTGCGAGACCTACAGTGAGCAGGGACGAAAGGGGCTTAGTGATCCGGCGGTTCCGGTGGAAGGGCCGTCGCTTAACGGATAAAGCTACCCTGGGATA ACAGGCTAATCTCGCCCAAGAGTTCACATCGACGGCGAGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGAGCTGAATTAGGTTCAAGGGTTGGCTG TCCGCCCATAAAGCGGTACGCGAGCTGGGTTCAGAACGTGTGAGACAGTTCGGTCCCTATCTGTTGTGGGCGTAGGAAATTGAGGAGCCTGTCCCTAGTA CGAGAGGACCGGGATGGACATACGCTGGTGTACCAGTTGTTCTGCCAAGACACGCTGGGTAGCTAAGTTGGCTGGATAAGCGCTGAAACATCTAAGCACA AGCCACTCAAGAGAGATTTCCCAGACCCCTGAGAGACGATAGGTGATGGTCAG Bartonella TGCTTAAGGCATTTGGTGGATGCCTTGGCATGCAGGCGATGAAGGACGTGATACCTGCGATAAGCTACGGGGAGGTGCGAAACCCTTGATCCGTAGATTT CCGAATGTCTAAATGAGCGACGCAGGGACTGAAACATCTAAGTACCTGTGGAAAGGACATCAACGAGACTCCGTTAGTAGTGGCGAGCGAACGCGGACCA GGCCGCTAAAAGTAGAATCGATTGGAAATCGAACCAAGAGGTGAAGTCCCGTAACAAACCTGAGTAGGCGGGACACGTGAAATCCTGTCTGAACATGGGT CGACCACGATCCAAGCCTAAGTACTCTGCATGACCGATAGCGCACAGTACCGTGAGGAAAGGTGAAAAGTCCGGAGTGAAAAGACTGAAACCGAATGCCT ACAACAGTCGGAGCCCTGGGTGACGGGTACCTTTTGTATAATGGGTCAGCGACTTAGTCTAACGAGCAGCTTAAGATGGTAGGCGTAGCGAGCGGTCTGA ATAGGGCGCAGTTCGTTGGATTAGACCCAAACCAGTGATCTAGCCATGAGCAGCTGAAGGTAAGTAACACTTACTGGAGGGCCGAACGTATCTGTTGCAA TAGATGGGATGACTGTGCTAGGGGTGAAAGGCCAATCAAACTCGAAATAGCTGGTCTCCGCGAAATCTATTTAGGTAGAGCGTTAGTTTCTCCAGGGGTA GAGCACTGGATGGGCTAGGTCCCGATAAACCTAACCAAACTCCGAATACCTGAAACTGGCAGACACACGCGGGTGCTAACGTCCGTCGTGGAAAGGGCAA CAACCCTAACCACCATCTAAGTCCCCAAGTTGGCTAAGTGGAAAGGATGTAGGATCCCAAAACAACCAGGATGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAACAGCTCACTGGTCTAGGGTCTTCCGAAAATGTCGGCTAAGCCATACACCGAAGCTGTGGATTAGTGGTAGCGGAGCGTTCCGTACCTGTAAGGGG ACTCGCGAAGCTCCTGGAGGTATCGGAAGTGAGAATGTGACATGAGTAACGAAAGGGAGTGAGAGACTCCCTCGCCGAAAGTCCAAGGTTCCTGCTTAAG TTAATCTGAGCAGGGTGAGTCGGCCCCTAAGGCGAGGCCGAACGTAGTCGATGGGAACCACGTAATATTGTGGACGTGACGGATTAGGAAATTGTAGGTA TTGATCTCAGTAATCCCAGGAAATACACCGTACCAAACCGACACAGGTGGACGGTAGAGAATACCAAGGCGTTGAGAGAACTACGTTGAAGGAACTCGGC AAATTGCACGCGTAACTTCGGAAGAAGCGTGACCCTCAGGGTGGCACAGACCGGGGGAGGACTGTTTACCAAAAACACAGGCTCTGCGAAGTCGCAAGAC ATGTATAGGGTCTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGAGATGTCAAGATTGAATTGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCCCCGCTGTCTCCAACGTAGACTCAGTGAAATTGAATTCCC CGTGAAGATCGGGGTTCCTGCGGTTAGACGGAAGACCCCGGCACCTTTACTATAGCTTTACACTGGCATTTGTGTCGGCATGTGTAGGATAGGTGGTAGA CTTTGAAGCAGGGGCGCTAGCCCTTGTGGAGTCTCCTGAAATACCACCCTTACCGACATGATGTCTAACTGCAATTTCAAGACAGTGTATGGTGGGTAGT TTGACTGGGGCGGTCGCCTCCTAAAGAGTAACGGAGGCGCGCGAAGGTAGGCTCAGAACGGTCGGAAATCGTTTGTTGAGTGCAATGGCATAAGCCTGCC TGACTGTGAGACTGACAGTGAGCAGAGTCGAAAGGGTCATAGTGATCCGGTGGTCCCGGTGGAAGGGCCATCGCTCAACGGATAAAGGTACGCCGGGATA ACAGGCTGATGACCCCCAAGAGTCCATATCGACGGGGTGTTTGGCACCTCGATGTCGACTCATCGCATCCTGGGGCTGGAGCAGGTCCAAGGGTATGCTG TTCGCCATTAAAGCGGTACGTGAGTTGGGTTCAGAACGTGTGAGACAGTTCGGTCCCTATCTGCCGTGGGTGTAGGAATTTGACAGGACTGTCCCTAGTA CGAGAGGACCGGGATGGACGTATTCTGGTGGACCTGTTGTGGCGCCAGCCCAAGCAGGGTAGCTATATCGGCGGGATAACCGCTGAAGCATCTAAGCGGA AACCCCCTAAAAGAGTATTCCCAGAACCGTGGTAGACCACACGTGATGGTCAG Chlamydophila@felis TTAGTAAGGCTATTGGCGGATGCCTTGGCATTGAGGCGATGAAGGATGCGTTTACTGCAGTAATCTTCGGCGAGCTGGTATAAGCTAGACCCGGAGGTCT CCGAATGTTAACATAAGCGACCTGCTGACTGAAACATCTTAGTAAGCAGGGAAAAGAAATCAAAGAGATTCCCTGAGTAGCGGCGAGCGAAAGGGGATTA GACCGGGTTTAGTTGAATCTTCTGGAAATAGAACGCACAGGTGAAGTCCCGTAACAAACCTGAGTGGGCTAGACACGTGAAACCTAGTCTGAATCTGGGG AGACCACTCTCCAAGTCTAAATACTATCAATGACCTATAGTGAACAGTACTGTGAAGAAAGGTGAAAAGACTTGAGTGAAAAGACTGAAACCAATAGCTT ATAACGGTCGAAGACCCGGTTGACGGGTGCCTTTTGCATGATGAGCCAGGGAGTTAAGTTAAACGGCGGGTTAAGTACGGAGCCGAAGCGAGCGGTTTTA ATAGAGCGTAGTCGTTTGATTTAGACACAAACCAGTGAGCTATTTATGACCAGTTGAAGCGTGGTAAGACCTTGTGGAGGACCGAAAGTACATGTTGAAA AATGTTGGATGAGTGTAATAGGGGTGAAAGGCCAATCAAACTTGAGATATCTTGTCTCTCCGAAATAACTTTAGGGTTAGCCTCGGAATTTTTTGGGGTA GAGCACTGAATTCTAGCGGGCTCGCTAACGGAAATCAAACTCCGAATACCAAGATCCGGGAGATAGACGCGGGGGCTAAGCTTCGTTGTCGAGAGGGGAA CAGCCCAGACCGCCGATTAAGTCCCAAATTATGCTAAGTGATAAGGAAGTGTGATTCTAAGACAGTTGGAATGTTGCTTAGAGGCAGCATTTAAAGAGTG CGTAACAGCTCACCAATCGAGAATCATCCAATAATAACGGCTAAGCATAAAACCGACATCGCGGGTTAGCGGTAGGAGAGCGTAGCATTGCAGTAAGGTA TACCGTAAGAGTGCTGGAGCGGATGCTAGTGAAGATCTGGCATAAGTAACGAAAGGAAGTGAAAATCTTCCTCGCCGTAAGCACAAGGTTCCAGGGTCAG CTCGTCTTCCCTGGGTTAGTCGGCCCCTAAGTCGAGGCACAACGTAGACGATGGACAACAGGTAATATTCTGTACATGACGGAGACGTTAAGCACCGGAT TGGTCCGGTGTCCTTTCAAGAAATATACCGTACCAAACCGACACAGGTGTGCAGATGAATATTCTAAGGCGGCGAGATAACTTTCGTTAAGGAACTCGGC AAATTATCCCCGTAACTTCGGAAGAAGGGGAGCCTTTTGAGCCGCAGAGAAAGGCCCGGGACTGTTTAACAAAAACACAGCCTATGCAAACCTCTAAGGG AAGTATATGGTGTGACGCCTGCCCAATGCCAAAAGGTTAAAGGAATATGTCAAGATTGAACCCAAGCCCTGGTGAATGGCCGCCGTAACTATAACGGTGC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGTGTAACGATCTGGGCACTGTCTCAACGAAAGACTCGGTGAAATTGTAGTAGC AGTGAAGATCTGTTTACCCGCAAAAGGACGAAAGACCCCGGAACCTTTACTGTACTTTGGTATTGATTCTTGATTTGTTATGTGTAGCATAGCCAGGAGA CTGTGAACACTCTTCGTTAGGAGAGTGGGAGTCTCGTGAAATACTGGTCTTAACAAGTTGGAGTCTAACATAAATATATGGACATTGCCAGACGGGCAGT TTTACTGGGGCGGTATCCTCCTAAAAAGTAACGGAGGAGCCCAAAGCTTATTTCATCGTGGTTGGCAATCACGAGTAGAGCGTAAAGGTATAAAATAGGT TGACTGTAAGACCTACAGTAAGCAGAGACGAAAGGGGCTTAGTGATCCGGCGGTGGAAGTGGAATCGCCGTCGCTTAACGGATAAAGGTACTCCGGGATA ACAGGCTGATCGCCACCAAGAGTTCATATCGACGTGGCGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGGGCTGGAGAAGGTCCAAGGGTTTGCTG TTCGCCAATAAAGCGGTACGCGAGCTGGGTTCAAAACGTGTGAGACAGTTTGGTCTCTATCCTTTGTGGGCGCAGGATATTGAAAGGACTGTTCCTAGTA CGAGAAGGCCGGAATGGACGAACAATGGTGTGTCGGTTGTTTTGCCAAAACAAGCCGAGTAGCTACGTCGGAAGGATAAGCATTGAAACATCTAAATGCA AGCCTCCTAAGAAAGGTATCCCAGACTCCATATAGACTATTGGTGATGGTTGG Brucella TGCTTAAGGCATTTGGTGGATGCCTTGGCATGCAGGCGATGAAGGACGTGATACCTGCGATAAGCGTCGGGGAGGTGCGAAACCCTTGATCCGACGATTT CCGAATGTCTACATGAGCGACCTGGGGACTGAAACATCTAAGTACCCAGGGAAAGGACATCAAAGAGACTCCGCTAGTAGTGGCGAGCGAACGCGGACCA GGCCGCTTAAAGTGGAACGAGTTGGAAACTCGACCAAGTGGTGAAGTCCCGTAACAGACCTGAGTGGGCGGGACACGTGAAATCCTGTCTGAACATGGGT CGACCACGATCCAAGCCTAAGTACTCTGCATGACCGATAGCGAACAGTACCGTGAGGAAAGGTGAAAAGCCCGGAGTGAAAAGACTGAAACCGGATGCCT ACAACAGTTGGAGCCCTGGGTGACAGGTACCTTTTGTATAATGGGTCAGCGACTTAGTGTATCGAGCAGCTTAAGGTGGTAGGCGCAGCGAGCGGTCTGA ACAGGGCGCAGTTCGATGCATTAGACCCAAACCAGTGATCTAGCCATGAGCAGTTGAAGGTACGTAACACGTACTGGAGGACCGAACATATCTGTTGCAA TAGATGGGATGACTGTGCTAGGGGTGAAAGGCCAATCAAACTTGAGATAGCTGGTCTCCGCGAAATCTATTTAGGTAGAGCGTCGACTACCCCCGGGGTA GAGCACTGGATGGGCTAGGGACCTCTAATCCTAACCAAACTCCGAATACCGGTAGTCGGCAGACACACGCGGGTGCTAACGTCCGTCGTGGAGAGGGCAA CAACCCTGACCACCATCTAAGTCCCTAAGTTGGCTAAGTGGAAAGGATGTAGGATCCCAAAACAACCAGGATGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAACAGCTCACTGGTCTAGGGTCTTCCGAAAATGTCGGCTAAGCCATACACCGAAGCTGTGGATTAGTGGTAGCGGAGCGTTCCGTACCTGTAAGGGC AGTCGTGAACATCCTGGAGGTATCGGAAGTGAGAATGTGACATGAGTAACGAAAGGGAGTGAGAGACTCCCTCGCCGAAAGTCCAAGGTTCCTGCTTAAG TTAATCTGAGCAGGGTTAGCCGGCCCCTAAGGCGAGGCCGAACGTAGTCGATGGGAACCACGTAATATTGTGGGCGTGACGGATCGCGTGGTTGTAGGTA TTGATCTCAGCGGTTCCAGGAAATACACCGTACCAAACCGACACTGGTGGACGGTAGAGAATACCAAGGCGTTGAGAGAACTGCGTTGAAGGAACTCGGC AAAATGCACGCGTAACTTCGGAAGAAGCGTGACCTCCAGGGTGGCACAGACCGGGGGAGGACTGTTTACCAAAAACACAGGCTCTGCGAAGTCGCAAGAC ACGTATAGGGTCTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGAGAGGTCAAGCTTGAATTGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCCCCGCTGTCTCCAACGCAGACTCAGTGAAATTGAATTCCC CGTGAAGATCGGGGTTCCTGCGGTTAGACGGAAGACCCCGGCACCTTTACTATAGCTTTACACTGGCATTCGTGACGACATGTGTAGGATAGGTGGTAGA CTTTGAAGCAGGGGCGCCAGCCTTTGTGGAGTCCCCTGAAATACCACCCTTGTTTTTATGATGTCTAACTGCGATTCCAGGACCGTGTATGGTGGGTAGT TTGACTGGGGCGGTCGCCTCCTAAAGAGTAACGGAGGCGCGCGATGGTAGGCTCAGAACGGTCGGAAATCGTTCGTCGAGTGCAATGGCATAAGCCTGCC TGACTGCAAGACTGACAGTGAGCAGAGACGAAAGGGTCATAGTGATCCGGTGGTCCCGGTGGAAGGGCCATCGCTCAACGGATAAAGGTACGCCGGGATA ACAGGCTGATGACCCCCAAGAGTCCATATCGACGGGGTGTTTGGCACCTCGATGTCGACTCATCGCATCCTGGGGCTGGAGCAGGTCCAAGGGTATGCTG TTCGCCATTAAAGCGGTACGTGAGTTGGGTTCAGAACGTGTGAGACAGTTCGGTCCCTATCTGCCGTGGGTGTAGGAATTTGACAGGACTGTCCCTAGTA CGAGAGGACCGGGATGGACGTATTCTGGTGGACCTGTTGTGGCGCCAGCCCAAGCAGGGTAGCTATATCGGCGGGATAACCGCTGAAGCATCTAAGCGGA AACCCCCTAAAAGAGTATTCCCAGAGCCGTGGAAGACCACACGTGATGGCCGG Thermus ATGGTAAGGCCCACGGTGGATGCCTCGGCACCCAGCCGATGAAGGACGTGGCTACTGCGATAAGCCAGGGGGAGCCGGTAGGGGCGTGATCCCTGGATGT CCGAATGCCGTTTTGGGGGACCTGGGGACTGAAACATCTCAGTACCCAGGGAGAGGAAAGAGAATCGACTCCCTGAGTAGCGGCGAGCGAAAGGGGACCA GCCTGGGCCTAGCCGAAGCTGTTGGGAACAGCGCCGAGAGGTGAAGCCCCGTAGCAAGCCCGAGTCCCCGTGGTTCGTGGAGCCATGGGGGAATCTGGGC GGACCACGGCCTAAGGCTAAGTACTCCGGGTGACCGATAGCGCACAGTACCGTGAGGAAAGGTGAAAAGACCGGAGTGAAAAGGCTGAAACCGTGGGCTT ACAACAGTCACGGCCCAGGGTTGTGGGTGCCTATTGAAGCATGAGCCGGCGACTCACGGTCGTGGGCGGCTTAAGTTGGGAGGCGTAGGGACCGGTCCGA ACAGGGCGAAGTCCGCGGCCGTGGACCCAAACCGGCGAGCTAGCCCTGGCCAGGTGAAGCTGGGTGAGACCCAGTGGAGGCCCGAAGGTGGGGGATGCAA ACCCCCGGATGAGTGGGCTAGGAGTGAAAAGCTAACCGAGCCCGAGATAGCTGGTCTCCCCGAAATGACTTTAGGGTCAGCCTCAGGGACTGGGGCTGTA GAGCACTGATAGGGCTAGGGCCCGCCAAACCCTGTCAAACTCCGAAGGGTCCTGCCTGGGAGTGAGGGGCGAGCGATAACGTCCGCGTCCGAGGCGGGAA CAACCGAGACCGCCAGCTAAGCCCCCAAGCGGGCTAAGTGGAAAGGATGTGCGCCGCGAAGACAGCCAGGAGGTTGCTTAGAAGCAGCCTTTAAAGAGTG CGTAATAGCTCACTGGTCGAGTGGCGCCCGAAAATGACGGCTAAGCCCAGCGCCGAAGCTGCGGGTATGCGGTAGGGGAGCGTTCCCGACCGATAAGGCG ACCCGCGAGGCGGCTGGAGGTAAGGGAAGTGCGAATGCGGCATGAGTAACGAAAGAGGGTGAGAATCCCTCTCGCCGTAAGCCCAAGGTTCCTACGCAAG GTCGTCAGCGTAGGGTTAGGCGGGACCTAAGGTGAAGCCGAACGTAGCCGAAGGGCAGCCGGTAATATTCGGCCCGGGACGCTCAGGCTAGGGGGCGGAA TGGCCCGCCCCCGAGCCAAGAAAAGCCCCGTACCAAACCGACACAGGTGGGCGGTGAAGAGCACTCAGGCGGCGGGAGAACCCTCGCCAAGGAACTCTGC AAGTTGGCCCCGTAACTTCGGGAGAAGGGGTGCTCCATGGGCCGCAGTGAACGGCTCGGGACTGTTTACCAAAAACACAGCCTCTGCGAACTCGTAAGAG AGGTATAGGGAGCGACGCTTGCCCGGTGCCGGAAGGTCAAGGGGAGGGGTCAAGCCCGAACCGAAGCCCCGGTGAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAAAAGCGTAACGACCGGAGCGCTGTCTCGGCGAGGGACCCGGTGAAATTGAACTGGC CGTGAAGATCGGCCTACCCGTGGCAGGACGAAAGACCCCGGGAGCTTTACTGCAGCCTGGTGTTGGCTCTTGGTCGCGCCTGCGTAGGATAGGTGGGAGC CTGTGAACCCCCGCCTCCGGGTGGGGGGGAGGCCCGTGAAATACCACCCTGGCGCGGCTGGGGCCTAACCCTCATGGGGGGACAGCGCTTGGCGGGCAGT TTGACTGGGGCGGTCGCCTCCTAAAAGGTAACGGAGGCGCCCAAAGGTCCCCTCAGGCGGGACGGAAATCCGCCGGAGAGCGCAAGGGTAGAAGGGGGCC TGACTGCGAGGCCTGCAGCGAGCAGGGGCGAAAGGGGCCTAGTGAACCGGTGGTCCCGGTGGAAGGGCCATCGATCAACGGATAAAGTTACCCCGGGATA ACAGGCTGATCTCCCCCGAGCGTCCACAGCGGCGGGGAGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGAAGAAGGTCCAAGGGTTGGCTG TTCGCCCATAAAGCGGCACGCGAGCTGGGTTCAGAACGTGTGAGACAGTTCGGTCTCTATCCGCCACGGGCGCAGGAGGTTGAGGGGGCTCTTCCTAGTA CGAGAGGACCGGAAGGGACGCACTCTGGTTTCCCAGCTGTCCCTCCAGGGCAAGCTGGGTAGCCATGTCGGAGGGATAACCGCTGAAACATCTAAGCGGA AGCCCCCCAAGAGAGGCCTCCCAGGACCCGGGAAGACCACCGGTGATGGCCGG Streptomyces@griseus TTTTTAAGGCGCACGGTGGATGCCTTGGCACCAAACCGATGAAGGACGTGGGAGCCACGATAGTCCCCGGGGAGCTGCAACAAGCTTGATCCGGGGGTTT CCGAATGCCCACATGGGGGACGAGGGGAGTGAAACATCTCAGTACCCTCGGAAGAGAAAACAACGTGATTCCGGGAGTAGTGGCGAGCGAAACTGGATGA GGCCGGATGTAGGCGAAGACATGCGAAAGTCCGGCTAGAGGTAAACCCCCGTACTAACCCCAAGTGCACGGGGCCCGAGAAATCCCGTGTGAATCTGGCG GGACCACCCGCTAAGCCTAAATATTCCTGGTGACCGATAGCGGATAGTACCGTGAGGAATGGTGAAAAGTGCGGAGTGAAAAGACTGAAACCGTGTGCCT ACAACCGTGGGAGCGTTTCGTGACTGGTGCCTTTTGAAGAATGAGCCTGCGAGTTAGGGTGTGTAGCGGGTTAACTGGGAAGCCGTAGCGAGCGGTCCGA ACAGGGCGGAGTTGCACGCTCTAGACCCAAGCGAGTGATCTAGCCATGGGCAGTTGAAGCGGAGTAAGACTTCGTGGAGGACCGAACACCAGGGTTGAAA ACCTGGGGATGACTGTGTTAGGGGTGAAAGGCCAATCAAACTCGTGATAGCTGGTCTCCCCGAAATGCATTTAGGTGCAGCGTCGTGTTCTGCCGAGGTA GAGCACTGGATAGGCGAGGCCTCGGTAACCTTAGCCAAACTCCGAATGCCGGAGCACGGCAGTGAGACGTGGGGGATAAGCTCCATGGTCGAGAGGGAAA CAGCCCAGAGCATCGACTAAGCCCCTAAGGACGCTAAGTGGAAAGGATGTGAGTCGCAGAGACAACCAGGAGGTTGCTTAGAAGCAGCCTTGAAAGAGTG CGTAATAGCTCACTGGTCAAGTGATTCCCGACAATGTCGGCTAAGCGTACCGCCGAAGTCGTGTCAAATGGGTAGGGGAGCGTCGTGTGCGGGTAAGCAG CCGCGGAACGGTTGTGGACGGTTCACGAGTGAGAATGAGGCATGAGTAGCGAACACACGTGAGAAACGTGTGCGCCGATTGACTAAGGTTCCTGGGTCAG CTGATCTGCCCAGGGTAAGTCGGGACCTAAGGCGAGGCCGAACGTAGTCGATGGACAACCGGTGATATTCGGTACGTGACGCAGAAGGTAGTCCACCCGG TGGCGGGGGATTCTGTCGAGAAAAGCCCCGTACCAAACCGACTCAGGTGGTCGGTAGAGAATACCGAGGCGTCGGGTGAACTATGGTTAAGGAACTCGGC AAAATGCCCCCGTAACTTCGGGAGAAGGGGGGCCATTTGTGCCGCAGAGACCGCGAGAGGACTGTTTACTAAAAACACAGGCCGTGCGAAGCCGTAAGGC ATGTATACGAACTGACGCCTGCCCGGTGCTGGAACGTTAAGGGGACCGGTTCGGTGAGAACTTAAGCGCCAGTAAACGGCGGTGGTAACTATAACCATCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCTCGACTGTCTCAACCATAGGCCCGGTGAAATTGCACTACG AGTAAAGATCTCGTTTCGCGCAGCAGGACGGAAGACCCCGGGACCTTTACTATAGTTTGATATTGGTGTTCGGTTCGGCTTGTGTAGGATAGGTGGGAGA CTTTGAAGCGGCCACGCCAGTGGTTGTGGAGTCTCGTGAAATACCACTCTGGTCGTGCTGATGTCTAACCTGGATTCAGGGACAGTGTCTGATGGGTAGT TTAACTGGGGCGGTTGCCTCCTAAAGAGTAACGGAGGCGCCCAAAGGTTCCCTCAGCCTGGTTGGCAATCAGGTGTTGAGTGTAAGTGCACAAGGGAGCT TGACTGTGAGACCGACGGTGAGCAGGGACGAAAGGGGACTAGTGATCCGGCAGTGGCTGTGGAAGCGCTGTCGCTCAACGGATAAAGGTACCCCGGGATA ACAGGCTGATCTTCCCCAAGAGTCCATATCGACGGGATGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGTCGGTCCAAGGGTTGGCTG TTCGCCCATAAAGCGGTACGCGAGCTGGGTTTAGAACGTGTGAGACAGTTCGGTCCCTATCCGCTGTGCGCGTAGGAATTTGAGAAGGCTGTCCCTAGTA CGAGAGGACCGGGACGGACGAACTCTGGTGTGCCAGTTGTCCTGCCAAGGCAGGCTGGTTGGCTACGTCGGAAGGATAACCGCTGAAACATCTAAGCGGA AGCCTCTTGAGAGAGTATTCCCAGGCTCCCAGTAGACGACGGGTGATGGCCAG Alcaligenes CGAATAAGGCATATGATGGATGCCTTGGCGATCAGGCGATGAAGGACGCGGTAGCTGCGAAAAGCTACGGGGAGCTGCAAAAAGCTTGATCTGTAGATGT CCGAATGTCCACATGAGCGACCGAGTGACTGAACCATCTCAGTAACTCGGGAAAAGAAATCAACGAGATTCCGGAAGTAGTGGCGAGCGAAACCGGACCA GCCTATGAATAGTCGAATGGAATGGAAATCCAGCCTAGCGGTGAAGCCCTGTAGCAATAACAAGTGGGCGGGACACGTGAAATCCTGTCTGAATATGGGG GGACCATCCTCCAAGGCTAAATACTCTGATCGACCGATAGTGAACAGTACCGTGAGGAAAGGCGAAAAGACCGGAGTGAAAAGTCTGAAATCGTATGCAT ACAACAGTAGGAGCACCGTGTGACTGGTACCTTTTGTATAATGGGTCAGCGACTTACATTCAGTGGCAGCTTAACAAGGGAGGCGTAGCGAGCGGTCCGA ATAGGGCGCAGTCGCTGGGTGTAGACCCAAACCGGCGATCTATCCATGGCCAGTTGAAGGCACGTAACACGTGCTGGAGGACCGAACACTAATGTTGAAA AATTAGGGATGAGTGTGATCGGAGTGAAAGGCTAAACAAGCCTGAGATAGCTGGTCTCTCCGAAAACTATTTAGGTAGTGCCTCGTATACTGCCGGGGTA GAGCACTGTTATGGCTAGGGTCGACTAACCCATGGCAAACTCCGAATACCGGTATACGGGAGACAGAGACGGGTGCTAACGTCCGGACTCAAGAGGGAAA CAACCCAGACCGCCAGCTAAGTCCCTAACATGGCTAAGTGGAAACGAAGTGGAAGGCATAGACAGTCAGGAGGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAATAGCTCACTGATCGAGTCGTCCCGGAAGATGTCGGCTAAGCCATAGACCGAAGCTGCGGATATATGGTAGGAGAGCGTTCCGTACCTGTAAGGTG TTCCGTGAGAATGCTGGAGGTATCGGAAGTGAGAATGTGACATGAGTAGCGAAAGGGGGTGAAAAGCCCCCTCGCCGTAAGTCCAAGGTTCCTGCGCAAG TTCATCGGCGCAGGGTGAGTCGGCCCCTAAGGCGAGGCAGAACGTAGCTGATGGGAAGCGGGTAATATTCCGCACGGGACGGATTGCAGATGTTACGGGT TGGCCCGAACTCGTTCCAAGAAAAGCACCGTACCAAACCGACACAGGTGGACGGGAGAATATTCCAAGGCGTTGAGAGAACTCAGGAGAAGGAACTCGGC AAATTAATACCGTAACTTCGGGAGAAGGTATGCCTCGCAAGCCGCAGTGAATGGTGGTGGACTGTTTACTAAAAACACAGCCTCTGCAAACACGAAAGTG ACGTATAGGGTGTGACGCCTGCCCGGTGCCGGAAGGTTAAGTGATGGGGTCAAGTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGATGGCCACACTGTCTCCTCCTGAGACTCAGCGAAGTTGACATGGT TGTGATGATCAATCTCCCCGCGGCTAGACGGAAGACCCCAGAACCTTTACTGTAGCTTTGCATTGGATTGTGAACCGGCCTGTGTAGGATAGGTGGGAGA CGTTGAAGCGTGGTCGCCAGATCGCGTGGAGTCTCCTGAAATACCACCCTGGTCTGTTTGGGTTCTAACCTAGATTCGGGGACCGTGCATGGTGGGCAGT TTGACTGGGGCGGTCTCCTCCTAAAGTGTAACGGAGGAGTTCGAAGGTACGCTAGAGACGGTCGGAAATCGTCTTGATAGTGCAATGGCATAAGCGTGCT TGACTGTGAGACTGACAGTGAACAGGTACGAAAGGGACATAGTGATCCGGTGGTTCTGATGGAAGGGCCATCGCTCAACGGATAAAGGTACTCTGGGATA ACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGGTTTGGCACCTCGATGTCGGCTCATCTCATCCTGGGGCTGTAGCCGGTCCAAGGGTATGCTG TTCGCCATTAAAGAGGTACGTGAGCTGGGTTTAAAACGTGTGAGACAGTTTGGTCCCTATCTGCCGTGGGCGTTGGATATTGACGGAGCTGCTCCTAGTA CGAGAGGACCGGAGTGGACGTACACTGGTGTATCGGTTGTCATGCCAATGCATGCCGAGTAGCTACGTCGGAGAGATAACCGCTGAAGCATCTAAGCGGA AACTCTCTAAGATAGATATCCCAGGGTCGTCCGAGACCAGACGTGATGGCTGG Mycoplasma@hyopneumo TAAATAAGGTATTTGGTGGATGCCTTGGGTCTGAGTCGATGAAGGACGTGATTACTGCGATAAGCTTCGTGGAGTTGGAAAAAACTAGATACGGAGATTT CCGAATGCGCTCATAGAGAACGTTGCGATTGAAACATCTTAGTAGCAACGGAAAAGAAAATAAAATGATTCCCAAAGTAGTGGCGAGCGAAATGGGAAGA GCCCGGAAATAGTAGAAAAAGTTGGAAACTTTGACTAGAGGTGAATCCCTGTAATAATCCTGAGTGGGCGGGGCACGTGGAACCCTGTCTGAATTTGCCA GGACCACCTGGTAAGGCTAAATACTATCAGACACCGATAGTGAATAGTACCGTGAGGAAAGGTGAAAAGACCGGAGTGAAAAGTCTGAAACCATTTACTT ACAATAGTCAAAGCACAGTGTGATGGGTACATCTTGCAGTATGGTCCGGCGAGTTATGTTAACAAGCAGGTTAAGATGGGAGCCGTAGGGACCGGTCTAA ATAGGGCGAAGTTTGTTGACATAGACCCAAACCGGTGATCTATCCATGAGCAAATGAAACTTTGTAACACAAAGTGGAGGTTCGAAGTAGTACGCTAAAA AGTGCCGGATGACTGTGATAGCGGTGAAATTCCAATCGAACCTGAGATAGCTGGTCTCTCCGAAATAGCTTTAGGGCTAGCGTATAGTAATAATGGGGTA GAGCACTGAATGTGGAAGCGGCTCTGAACTATAATCAAACTCCGAATACCATCTCTATGCAGTCGGAAGTGGGTGATAACGTCCGCGCTCGCGAGGGAAA CAACCCAGATCGTCAGCTAAGTCCCAAAATATGTTAAGTGAAAAGGTTGTAAATTTCTTAAACAACTAGGATGTTGCTTAGAAGCAGCCTTTAAAGAGTG CGTAATTGCTCACTAGTCAAGAGATCTCCAATAATGTCGGCTAAACATAATACCGAAGCTGCGGGTTTACGTTAGGAGAGCGTTTTAATTCGCTAAGCTA GAGGGTGACACTAGTGGAGAAATTAAAAGTGAGAATGCGGAATGAGTAACGATTCGAAGTGAGAATCTTCGACGCCTATTGGGGAAGGTTCCTGGGCAAG GTCGTCCACCCAGGGTTAGTCAGGGCCTAAGGAGAGGCTGAACGTATCCGATGGATAATCGGTAATATTCGATACATTACGAAAAAGATAGTTTTCCACC TGGGTGGAAATTTTTCCAAGAAAAGTCCTGTACCGAACGGACACACGTCCCCAGATGAGTATTCTAAGGTGGCGAGAAAACCAATGTTAAGGAACTCTGC AAAATTATCCCGTACGTTCGCAAGAAGGGATGCCCTCTAGGCCTCAGTAAAAAGGGGGGAACTGTTTATCAAAAACACAGCCTCTGCAAAGGTGTAAACC AAGTATAGAGGGTGAAGCCTGCCCAGTGCCCGAAGGTTAAGCGGAGATGTATTGATTCAAGTGAAGCCCGGGTGAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCAACTAATTATTGACCTGCACGAAAGGCGCAATGATCTCCCTACTGTCTCAACATTGGACTCGGTGAAATTATGGTACC AGTGAAAACCTGGTTACCCGCATCAAGACGAAAGACCCCGGGAGCTTTACTATAACTTCGTATTGAGAATTGGTTTATTATGTGTAGGATAGGTGGGAGA TGTCGATCCAAGGGCGCTAGTCCTTGTGGAGTCAACTGAAATACCACCCTTAATAAATTGTTTTCTAACCTGCAAAGAGAGACAGTGCGTGGTGGGTAGT TTGACTGGGGCGGTCGCCTCCTAAAGAGTAACGGAGGTGTTCAAAGCTACACTCAATATGGTCGGAAACCATATGCAGAGCATAAAGGTAAAAGTGTGGT TGACTGCAAGACCTACAGTGAGCAGGTGCGAAAGGGACTTAGTGATCCGGCGGTTCATGTGGAATGGCCGTCGCTCAACGGATAAAGCTACCCCGGGATA ACAGGCTAATCTTCCCCAAGAGATCACATCGACGGGAAGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGAGCTGAAGTCGGTTCAAGGGTTTGCTG TTCGCCAATAAAGCGGTACGTGAGCTGGGTTCAGAACGTGTGAGACAGTTCGGTCCCTATCTGATGTGGGCGTTGGAATTTGATGAGACTGCTCTTAGTA CGAGAGGACCGGAGTGGACGTACGCTGGTGTTCCAGTTGTCTTGCCAAAGCAAGCTGGGTAGCTAAGTCGGAAAGATAACCGCTGAAACATCTAAGCGGA AGCTTCTCAAGAGAGTATTCCTAAATTCCTTATAGACTATAGGTGATGGTTAG Helicobacter@pilori CTTTTAAGGCAGATGGCGGATGCCTTGCCAAAGAGGCGATGAAGGACGTACTAGCTGCGATAAGCTATGCGGAGCTGTCAAGAGCTTGATGCGTAGATGT CCGAATGCTCTAATAGGCGACCTAGTGAGTGAAACATCTCAGTAACTAGGGAAAAGAAATCAACGAGATTCCCTAAGTAGTGGCGAGCGAACGGGGAAAA GGGCGGATTTAGCAGAGTTACCTGGAAAGTAAGCCTAGAAGTGAAGCCTTGTAGCCAACCAGAGTGGCCAGGACACGAGAAATCCAGGTTGAAGCCGGGG AGACCACTCTCCAACCCTAAATACTATCTTTGAGCGATAGCGAAAAGTACCGTGAGGAAAGGTGAAAAGAGCAGAGTGAAAAGACTGAAACCATCTGCTT ACAACATTCAGAGCCCTGGGTGATGGCTGCCTTTTGCATAATGATCCTGCGAGTTGTGGTATCTGGCAGGTTAAGAAGGAAGCCGTAGCGAGCGGTCTTA ATAGGGCGAAGTCAGATGCTGCAGACCCAAGCTAGTGATCTATCCATGGCCAGTTGAAACGCGTTAATAGCGCGTGGAGGACTGAACGTACCCATTGAAA CGGGTGGGATGAGTGTGATAGGGGTGAAAGGCCAAACAAACTTGTGATAGCTGGTCTCTTCGAAATATATTTAGGTATAGCCTCAAGAATAAAAGGGGTA GAGCCCTGATTGGGCTAGCTGCCCGGAAACCCTATCAAACTTCGAATACCTTTCCTTGGGAGTCAGGCGTGGGTGATAAAATCAATCGTCAAAAGGGGAA CAACCCAGACTACCAAATAAGTCCCTAAGTTATTCGAGTGGAAAAGATGTTGGCTACTCAAACAACCAGGAGGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAACAGCTCACTGGTCTAGTGGTCACTGAAAATATCGGCTAAGATAGACACCGAATTTGTAGATAAGTGGTAGAAGAGCGTTCATACGCGTTAAGGTA TACCGTAAGAGTGCTGGAGCGGTATGAAGTGAGCATGAGGAATGAGTAACGAAGATATATGAGAATTGTATCCGCCGTAAATCTAAGGTTCCTACGCGAG GTCGTCATCGTAGGGTTAGTCGGGTCCTAAGCCGAGTCCGAAGGTAGGTGATGGCAAATTGGTAATATTCAATACGGGACGCATGGGTTAAGCGACTAGA TGGCTAGCGCTCGTGCCAAGAAAAGTTCCGTACCAAACCGACACAGGTAGATAGATGAGTATTCTAAGGCGGTGAAAGAACTCTGGTTAAGGAACTCTGC AAACTAGCACCGTAAGTTCGCGATAAGGTGTGCCACCGTTGTCTCAGCAAAGGTCCCCCGACTGTTTACCAAAAACACAGCCTTTGCCAACTCGTAAGAG AAGTATAAGGTGTGACGCCTGCCCGGTGCTCGAAGGTTAAGAGGATGCGTCAAGGTTGAATTGAAGCCCGAGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGTTAAATACCGACCTGCATGAATGGCGTAACGAGATGGGAGCTGTCTCAACCAGAGATTCAGTGAAATTGTAGTGGA GGTGAAAATCCTCCTACCCGCGGCAAGACGGAAGACCCCGGGACCTTTACTACAACTTAGCACTGCTAATGGGAATATCATGCGCAGGATAGGTGGGAGG CTTTGAAGTAAGGGCTTTGGCTCTTATGGAGCCTCCTGAGATACCACCCTTGATGTTTCTTTAGCTAACTGGCATGGCAGGACAATGCTTGGTGGGTAGT TTGACTGGGGCGGTCGCCTCCTAAAAAGTAACGGAGGCTTGCAAAGGTTGGCTCATTGCGGTTGGAAATCGCAAGTTGAGTGTAATGGCACAAGCCAGCC TGACTGTAAGACATACAGTAAGCAGAGACGAAAGGGTCATAGTGATCCGGTGGTTCTGGTGGAAGGGCCATCGCTCAAAGGATAAAGGTACCCCGGGATA ACAGGCTGATCTCCCCCAAGAGCTCACATCGACGGGGAGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGGGCTGGAGCAGGTCCAAGGGTATGCTG TTCGCCATTAAAGCGGTACGCGAGCTGGGTTCAGAACGTGTGAGACAGTTCGGTCCCTATCTGCCGTGGGCGTAGGAAATTGAGGAGACTGTCCCTAGTA CGAGAGGACCGGGATGGACGTGTACTGGTGCACCAGTTGTTCTGCCAAGACACGCTGGGTAGCTACACCGGTGTGATAACTGCTGAAACATCTAAGCAGA AGCCACTCAAGAGAACTTTCCCAGCTCGCACAAAGACTATTGCTGATGGGTAG Bordetella@bronchise CGACTAAGGCATATGGTGGATGCCTTGGCGATCAGGCGATGAAGGACGTAGTAGCTGCGAAAAGCTGCGGGGAGCTGCAAAAAGCATGATCCGCAGATAT CCGAATGTCCACATGAGCGACCGGGTGACTGAAACATCTCAGTAGCTCGGGAAAAGAAATCAACGAGATTCCGAAAGTAGTGGCGAGCGAAATCGGAAGA GCCTACGCATAGTCGAACGGAATGGAAATCCGGCCTAGCGGTGAAGCCCTGTAACAATGAGAAGTGGGCGGGACACGTGAAATCCTGTCTGAAGATGGGG GGACCATCCTCCAAGGCTAAATACTCTGATCGACCGATAGTGAACAGTACCGTGAGGAAAGGCGAAAAGACCGGAGTGAAAAGTCTGAAACCGTATGCAT ACAACAGTCGGAGCCTTGGGTGACGGGTACCTTTTGTATAATGGGTCAGCGACTTACATTCAGTGGCAGCTTAACAAGGAAGGCGTCAGAAGCAGTCCGA ATAGGGCGCAGTCGCTGGGTGTAGACCCAAACCGATGATCTACCCATGGCCAGTTGAAGGCACGTAACACGTGCTGGAGGACCGAACACTAGTGTTGAAA AACTAGGGATGAGTGTGATAGGGGTGAAAGGCTAAACAAATCTGAAATAGCTGGTCTCTCCGAAAACTATTTAGGTAGTGCCTCAAGTACTGCAGGGGTA GAGCACTGTTATGGCTAGGGTTGACTAAACCATGGCAAACTCCGAATACCTGTACTTGGGAGACAGACACGGGTGCTAACGTCCGGACTCAAGAGGGAAA CAACCCAGACCGCCAGCTAAGTCCCGAATATCGCTAAGTGGAAACGAAGTGGAAGGCATAGACAGTCAGGAGGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAATAGCTCACTGATCGAGTCGTCCCGGAAGATGTCGGCTAAGCGATAAACCGAAGCTGCGGGTTTACGGTAGGAGAGCGTTCTGTACCTGCAAGGTG GCTTGTAAGGCTGCTGGAGGTATCAGAAGTGCGAATGTGACATGAGTAGCCAAAGGGGGTGAAAAGCCCCCTCGCCGTAAGTCCAAGGTTCCTGCGCAAG TTCATCGGCGCAGGGTGAGTCGGCCCCTAAGGCGAGGCAGAACGTAGCTGATGGGAAGCTGGTAATATTCAGCACGGGACGGATCGCGGAGGTCACAGGT TGGCCTGGATTTGTTCCAAGAAAAGCACCGTACCAAACCGACACAGGTGGGAGGGAGAATATTCCAAGGCGTTGAGAGAACTCAGGAGAAGGAACTCGGC AAATTGATACCGTAACTTCGGGAGAAGGTATACCCTGCAGGTCGCAGAGAATGGTGGTGGACTGTTTATTAAAAACACAGCCTCTGCAAAGACGAAAGTC ACGTATAGGGTGTGACGCCTGCCCGGTGCCGGAAGGTTAAGTGATGGGGTCAAGTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGATGGCCACACTGTCTCCTCCTGAGACTCAGCGAAGTTGAAGTGTT TGTGATGATCAATCTACCCGCGGCTAGACGGAAGACCCCAGAACCTTTACTGTAGCTTTGCATTGGACTGTGAACCGGCCTGTGTAGGATAGGTGGGAGG CGCAGAACTCGAGTCGCCAGATTCGAGGGAGCCTCCTGAAATACCACCCTGGTTTGTTTGGGTTCTAACCTTGATTCGGGGACAGTGCATGGTAGGCAGT TTGACTGGGGCGGTCTCCTCCCAAAGCGTAACGGAGGAGTTCGAAGGTACGCTAGGTACGGTCGGAAATCGTGCTGATAGTGCAATGGCATAAGCGTGCT TGACTGTGAGACTGACAGTGAACAGGTGCGAACGGGACATAGTGATCCGGTGGTTCTGATGGAAGGGCCATCGCTCAACGGATAAAGGTACTCTGGGATA ACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGGTTTGGCACCTCGATGTCGGCTCATCTCATCCTGGGGCTGAAGCAGGTCCAAGGGTATGCTG TTCGCCATTAAAGAGGTACGTGAGCTGGGTTTAGAACGTGTGAGACAGTTTGGTCCCTATCTGCCGTGGGCGCTGGAAATTGACAGGACTGCTCCTAGTA CGAGAGGACCGGAGTGGACGTACTCTGGTGTACCGGTTGTCATGCCAATGCATGCCGGGTAGCTAAGTCGGAGAGATAACCGCTGAAGCATCTAAGCGGA AACTCTCTAAGATAGGTATCCCAGGGTCGTTCGAGACCAGACGTGATGGTCGG Bacillus@stearotherm CTAGAAAGGCGCACGGTGGATGCCTTGGCACTAAGCCGATGAAGGACGGGGCAACGCCGAAACGCTCCGGGGAGCTGTAAGAAGCGTGATCCGGAGATGT CCGAATGTCCCCATGAGCAACCCGGGGACTGAAACATCTTAGTACCCGGGGAGAAGAAAGCAAAGCGATTCCCTGAGTAGCGGCGAGCGAAACGGGAACA GCCCGGAGGTAGACGAACGGTCTGGAACGCCGGCCGAGAGGTGAAGCCCTGTATCAACCCTGAGTCGGCGGGACACGGGAAATCCCGTCGGAAGCAGGGA GGACCATCTCCCAAGGCTAAATACTCCTAGTGACCGATAGTGCACAGTACCGTGAGGAAAGGTGAAAAGCCCGGAGTGAAAAGACTGAAACCGTGTGCCT ACAATAGTCAGAGCGCCGCGTGATGGGTGCCTTTTGTAGAATGAACCGGCGAGTGACGATGGCGTGCGGGTTAAGAAGGGAGCCGCAGCGAGCGGTCTGA ACAGGGCGAAGTACGTCGTCGTCGACCCAAACCGGTGATCTACCCATGTCCAGGTGAAGGCCGGTAACACCGGCTGGAGGCCCGAACACGCACGTTGAAA AGTGCGGGATGAGTGTGGTAGGGGTGAAATGCCAATCGAACTTGAGATAGCTGGTCTCCCCGAAATAGCTTTAGGGCTAGCCTCGGGAGATGTTGAGGTA GAGCACTGATTGGGCTAGGCCCTGGTAAACCCAGTCAAACTCCGAATGCCAATACCCGGGAGTCAGACGCGAGTGATAAGATCCGTGGTCGAGAGGGAAA CAGCCCAGATCGCCAGCTAAGCCCCAAAGGACGTTCAGTGGAAAGGATGTGAGTTGCAAAGACAACCAGGATGTTGCTTAGAAGCAGCCTTTAAAGAGTG CGTAATAGCTCACTGGTCGAGTGACTCCCGAAAATGTCGGCTAAACGTGCCGCCGAAGCTGCGGGATTTCGGTAGGGGAGCGTTCTAAGGCGTTAAGCCA GACCGGAAGACTGGTGGAGCGCTTAGAAGTGAGAATGCGGTATGAGTAGCGAACAGAGGTGAGAATCCTCTGCGCCGAAAGCCTAAGGTTCCTGAGGAAG TTCGTCCGCTCAGGGTTAGTCGGGACCTAAGCCGAGGCCGAACGTAGGTGATGGACAACAGGTGAGATTCTGTACGGGACGCAGAGGATAGGGCGCAGGC TGGCCTGCCCCCCTGCCAAGAAAAGCCCCGTACCAAACCGACACAGGTAGGCAGGAGAGAATCCTAAGGCGGCGGGAGAACTCTCGTTAAGGAACTCGGC AAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCGAAAGGCCGCAGACAAAGGCCCAAGACTGTTTATCAAAAACACAGGCTCTGCGAAGTCGTAAGGC ACGTATAGGGGCTGACACCTGCCCGGTGCTGGAAGGTTAAGGGGAGCGCTGAAGTGCGAACCGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCCGCACGAAAGGTGTAACGACTTGGGCGCTGTCTCAACGAGAGACCCGGTGAAATTATACTACC TGTGAAGATCAGGTTACCCGCGACAGGACGGAAGACCCCGGGAGCTTTACTGCAGCCTGATATGGAATTTTGGTGTCGCTTGTACAGGATAGGTGGGAGC CTGGGAAGCCGGAGCGCCAGCTTCGGTGGAGGCGCGTGGGATACCACCCTGGCGATATTGAATTCTAACCCGCAGTGGGAGACAGTGTCAGGCGGGCAGT TTGACTGGGGCGGTCGCCTCCCAAAAGGTAACGGAGGCGCCCAAAGGTTCCCTCAGAATGGTTGGAAATCATTCGGAGAGTGCAAAGGCACAAGGGAGCT TGACTGCGAGACGGACAGTGAGCAGGGACGAAAGGGGCTTAGTGATCCGGTGGTTCCGATGGAAGGGCCATCGCTCAACGGATAAAGCTACCCCGGGATA ACAGGCTGATCTCCCCCAAGAGTCCACATCGACGGGGAGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGGGCTGTAGTCGGTCCAAGGGTTGGCTG TTCGCCCATAAAGCGGTACGCGAGCTGGGTTCAGAACGTGTGAGACAGTTCGGTCCCTATCCGTCGCGGGCGCAGGAAATTGAGAGGACTGTCCTTAGTA CGAGAGGACCGGGATGGACGCACGCTGGTGTACCAGTTGTCCCGCCAGGGCACGCTGGGTAGCTATGTCGGCGGGATAAGCGCTGAAACATCTAAGCGTA AGCCCCCTAAGAGAGATTTCCCAGATCCCTCGAAGATGACAGGTGATGGTCCG Streptomyces@rimosus TTTTTAAGGCGCACGGTGGATGCCTTGGCACCAAACCCATGAAGGACGTGGGAGCCGCGATAGGCCCCGGGGAGCTGCAACGAGCTTGATCCGGGGGTGT CCGAATGCCCTCATGGGGGACGCGGGGAGTGAAACATCTCAGTACCCGCGGAAGAGAAAACAACGTGATTCCGGGAGTAGTGGTGAGCGAAACCGGATGA GGCCGGATGTAGGCGAAGACATGCGAAAGTCCGGCTAGAGGTAAACCCCCGTACTAACCCCAAGTGCACGGGGCCCGTGAAATCCCGTGTGAATCTGGCG GGACCACCCGTTAAGCCTAAATATTCCTGGTGACCGATAGCGGATAGTACCGTGAGGAATGGTGAAAAGTGCGGAGTGAAAAGACTGAAACCGTGTGCCT ACAACCGTGGGAGCGTTTCGTGACTGGTGCCTTTTGAAGAATGAGCCTGCGAGTTTGGGTATGTTGCGGGTTAACTGGGAAGCCGTAGCGAGCGGTCCGA AGAGGGCGTAGTAGCGTGCCCAAGACCCAAGCGAGTGATCTAGCCATGGGCAGTTGAAGCGGAGTAAGACTTCGTGGAGGACCGAACACCAGGGTTGAAA ACCTGGGGATGACTGTGTTAAGGGTGAAAGGCCAATCAAACTCGTGATAGCTGGTCTCCCCGAAATGCATTTAGGTGCAGCGTCGTGTTCTGCCGAGGTA GAGCACTGGATAGGCGAGGCCTCGGTAACCTTAGCCAAACTCCGAATGCCGGAGCGCGGCAGTGAGACGTGGGGGATAAGCTCCATGGTCGAGAGGGAAA CAGCCCAGAGCATCGACTAAGCCCCTAAGGGTGCTAGGTGGAAAGGATGTGAGTCGCAGAGACAACCAGGAGGTTGCTTAGAAGCAGCCTTGAAAGAGTG CGTAATAGCTCACTGGTCAAGTGATTCCCGACAATGTCGGCTAAGCACACCGCCGAAGTCATGTCAAATGGGTAGGGGAGCGTCGTGTGCGGGTAAGCAG CGCCGGAAGTGTTGTGGACGGTTCACGAGTGAGAATGAGGCATGAGTAGCGAACACACGTGGGAAACGTGTGCGCCGATTGACTAAGGTTCCTGGGTCAG CTGATCTGCCCAGGGTAAGTCGGGACCTAAGGCGAGGCCGAACGTAGTCGATGGACAACCGGTGATATTCGGTACGTGACGCAGAAGGTAGTCCACCCGG TGGCGGGGGATTCTGTCGAGAAAAGCCCCGTACCAAACCGACTCAGGTGGTCGGTAGAGAATACCGAGGCGTCGGGTGAACTATGGTTAAGGAACTCGGC AAAATGCCCCCGTAACTTCGGGAGAAGGGGGGCCACTTGTGCCGCAGAGACCGCGAGAGGACTGTTTACTAAAAACACAGGCCGTGCGAAGCCGTAAGGC TTGTATACGGACTGACGCCTGCCCGGTGCTGGAACGTTAAGGGGACCGGTTCGGTGAGAACTTAAGCGCCAGTAAACGGCGGTGGTAACTATAACCATCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCTCGACTGTCTCAACCATAGGCCCGGTGAAATTGCACTACG AGTAAAGATCTCGTTTCGCGCAGCAGGACGGAAGACCCCGGGACCTTTACTATAGCTTGATATTGGTGTTTGGTTCGGCTTGTGTAGGATAGGTGGGAGA CTGTGAAGCCGTGACGCCAGTCATGGTGGAGTCCTGTGAAATACCACTCTGGTCGTGCTGATGTCTAACCTGGATTCAGGGACAGTGTCTGGTGGGTAGT TTAACTGGGGCGGTTGCCTCCTAAAGGGTAACGGAGGCGCCCAAAGGTTCCCTCAGCCTGGTTGGCAATCAGGTGTTGAGTGTAAGTGCACAAGGGAGCT TGACTGTGAGACTGACGGTGAGCAGGTACGAAAGGGGACTAGTGATCCGGCGGTGGCTGTGGAAGCGCCGTCGCTCAACGGATAAAGGTACCCCGGGATA ACAGGCTGATCTTCCCCAAGAGTCCATATCGACGGGATGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGTCGGTCCAAGGGTTGGCTG TTCGCCCATAAAGCGGTACGCGAGCTGGGTTTAGAACGTGTGAGACAGTTCGGTCCCTATCCGCTGTGCGCGTAGGAGTTTGAGAAGGCTGTCCCTAGTA CGAGAGGACCGGGACGGACGAACTCTGGTGTGCCAGTTGTTCTGCCAAGGCAGGCTGGTTGGCTACGTCGGAAGGATAACCGCTGAAACATCTAAGCGGA AGCCTCTTGAGAGAGGGCTCCCAGGCTCCCAGTAGACGACGGGTGATGGCCAG Staphylococcus@pisci TTATTAAGGCGCACGGTGGATGCCTTGGCACTAAGCTGATGAAGGACGTTACTACGACGATATGCTTTGGGTAGCTGTAAGAAGCGTGATCCAGAGATTT CCGAATGTCGACATGAGCAACGCGGAGACTGAAACATCTTAGTACCCGCGGAAGAGAAAGAAAATCGATTCCCTGAGTAGCGGCGAGCGAAACGGGAAGA GCCCGGAATTAGACGAATGTACTGGAAATCGAACCGAGAGGTAAAGTCCTGTATCAAGCCTGAGTCGACGGAGCACGTGAAATTCCGTCGGAATCCGGGA GGACCATCTTCCAAGGCTAAATACTCCTAGTGACCGATAGTGAACAGTACCGTGAGGAAAGGTGAAAAGTCCGGAGTGAAAAGATTGAAACCGTGTGCTT ACAATAGTCAGAGCCCAGGGTGATGGGTGCCTTTTGTAGAATGAACCGGCGAGTTACGATCTGATGCAGGTTAAGCGGGGAGCCGCAGCGAGCGGTCTGA ACAGGGCGGAGTATTTGGTCGTAGACCCAAACCGGTGATCTACCCTTGGTCAGTTGAAGTTCAGTAACACTGAATGGAGGACCGAAGACTTACGTTGAAA AGTGACGGATGAATGAGGTAGCGGAGAAATTCCAATCGAACCTGAGATAGCTGGTCTCTCCGAAATAGCTTTAGGGCTAGCCTCAAGGATTGTTGAGGTA GAGCACTGTTTGGACGAGGCCTTGGTAAATTCAGACAAACTCCGAATGCCAATTCTTGGGAGTCAGAAGTGGGTGATAAGGTCCATGTTCGAAAGGGAAA CAGCCCAGACCACCAGCTAAGTCCCAAAAAATGTTAAGTGGAAAGGATGTGTATTGCCCAGACAACTAGGATGTTGCTTAGAAGCAGCCTTTAAAGAGTG CGTAATAGCTCACTAGTCGAGTGACACCCGAAAATGTCGGCTAAACATATTACCGAAGCTGTGGACTTGTGGTAGGAGAGCGTTCTAAGGCGTCAAGCAT GATCGCAAGACATGTGGAGCGCTTAGAAGTGAGAATGCGGTGTGAGTAGCGAAGATGGGTGAGAATCCCATCCACCGATTGACTAAGGTTCCAGAGGAAG CTCGTCCGCTCTGGGTTAGTCGGGTCCTAAGCCGAGGCCGAACGTAGGCGATGGATAACAGGTGATATTCTGTACGGGACACAGAGGATAGGCGACGTGT TGGCACGCGTTCCTGTCGAGAAAAGCCCCGTACCAAACCGACACAGGTAGTCAGATGAGAATTCTAAGGTGGCGAGAGAACTCTCGTTAAGGAACTCGGC AAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCTCAAGGCCGCAGTGAATGGCCCAAGACTGTTTATCAAAAACACAGGCTCTGCTAAACCGTAAGGT ATGTATAGGGGCTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGAGTGGTTCTGTACGAATCGAAGCCCCAGTAAACGGCGGCCGTAACTCTAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCCGCACGAAAGGCGTAACGATTTGGGCACTGTCTCAACGAGAGACTCGGTGAAATCATAGTACC TGTGAAGATCAGGTTACCCGCGACAGGACGGAAGACCCCGGGAGCTTTACTGTAGCCTGATATTGAAATTCGGCACAGCTTGTACAGGATAGGTAGGAGC CTTGGAAACGTGAGCGCCAGCTTACGTGGAGGCTTGTGGGATACTACCCTAGCTGTGTTGATTTCTAACCCGCATCGGGAGACAGTGTCAGGCGGGCAGT TTGACTGGGGCGGTCGCCTCCTAAAGTGTAACGGAGGCGCTCAAAGGTTCCCTCAGAATGGTTGGAAATCATTCATAGAGTGTAAAGGCATAAGGGAGCT TGACTGCGAGACCTACAGTGAGCAGGGTCGAAAGGGACTTAGTGATCCGGTGGTTCCGATGGAAGGGCCATCGCTCAACGGATAAAGCTACCCCGGGATA ACAGGCTTATCTCCCCCAAGAGTTCACATCGACGGGGAGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGGGCTGTAGTCGGTCCAAGGGTTGGCTG TTCGCCCATAAAGCGGTACGCGAGCTGGGTTCAGAACGTGTGAGACAGTTCGGTCCCTATCCGTCGTGGGCGCAGGAAATTGAGAGGACTGTCCTTAGTA CGAGAGGACCGGGATGGACATACTCTGGTGTACCAGTTGTCGTGCCAACGCACGCTGGGTAGCTATGTTGGCGGGATAAGTGCTGAAACATCTAAGCATA AGCCCCCTAAGAGAGATTTCCCAGATCCCTCAAAGATGATAGGTAATGGTTCG Microbispora TTACTAAGGCACACGGTGGATGCCTTGGCACCAAGCCGATGAAGGACGTGGGAGCTGCGATAAGCCTCGGGGAGCCGCTACAGGCGTGATCCGGGGATTT CCGAATGCCGGCATGGGGGACGCGGGGAGTGAAACATCTCAGTACCCGCGGAAGAGAAAGCAATGCGATTCCCTGAGTAGTGGTGAGCGAAAGGGGAAGA GGCTGGAGATAGCCGAACGCTCTGGAATGGCGGCCTAGACGTGAAGCCGGGTAGCAATCCCGAGTGCACGGGGCCCGAGGAATCCTGTGCGAATCTGCCA GGACCACCTGGTAAGCCTAAATACTCCTGGTGACCGATAGTGGAGAGTACCGTGAGGAAAGGTGAAAAGCCCGGTGTGAAAAGACTGAAACCGTGTGCCT ACAACCGTGGGAGCTTTATGTGACCGGTGCCTTTTGAAGAATGAGCCTGCGAGTTGACGTGCGTGGCGGGTTAACTGGGGAGCCGTAGCGAGCGGTCTGA ATAGGGCGGAGTCGCGTGCGTCAGACCCAAGCCGGTGATCTACCCGTGGGCAGGTGAAGCTCAGTAAGACTGGGTGGAGGCCCGAACACCAGGGTTGCAA ACCTGGGGATGACTGCGGTAGCGGTGAAAAGCCAATCGAACTCGTGATAGCTGGTCTCCCCGAAATGCATTTAGGTGCAGCGTCACGTCCTGCCGAGGTA GAGCACTGGTTGGCCGAGGCCCCGGTAAGGTCAGCCAAACTCCGAATGCCGGGACGTGGCAGTGAGACGCGGGGGATAAGCTTCGTGGTCGAGAGGGAAA CAGCCCAGATCACCGGCTAAGCCCCGAAGGGTGCTGAGTGGAAAGGATGTAAGCCGCTGTGACAGCCAGGAGGTTGCTTAGAAGCAGCCTCTAAGGAGTG CGTAATAGCTCACTGGTCTAGTGGTTTCCGACAATGTCGGCTAAGCACACCGCCGAAGCCGTGGCGTGCGGGTAGGGGAGCGTCGTGCGCGGGTAAGCGG CGGGGTGACCGCCGTGGACGCCGTGCGAGTGAGAATGAGGCATGAGTAGCGTTCAGAAGTGAGAAACTTCTGCGCCGGATGACCAAGGTTCCTGGGGCAG TTGATCCGCCCAGGGTAAGTCGGGACCTAAGGCGAGGCCGAACGTAGTCGATGGGCAACGGGTGATATTCCGTACGGGACGCAGAAGGTAGCCCACCCAG TGGTGGGGGGTTCTGCCGAGAAAAGCCCCGTACCAAACCGACTCTGGTGGTCGGTAGAGAATACCGAGGCGTCGGGCGAACCGCGGTTAAGGAACTAGGC AAATTGCCCCCGTAACTTCGGGAGAAGGGGGGCCTCGTGGGCCGCAGAGAATGGCCCGGGACTGTTTACTAAAAACACAGGCCGTGCGAAGTCGTAAGAC AAGTATACGGACTGACGCCTGCCCGGTGCCGGAACGTTAAGGGGACGGGTTCGGTCGGAACCTAAGCGCCGGTAAACGGCGGTGGTAACTATAACCATCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGGTCTGGGCACTGTCTCAACCGCGGACCCGGCGAAATTGCACTACG AGTAAAGATCTCGTTACGCGCAGCAGGACGGAAGACCCCGGGACCTTCACTGCAGCTTGGCATTGGCGTTTGGAATGGCTTGTGTAGGATAGGCGGGAGA CTGTGAAGCGGGCACGCCAGTGTCCGTGGAGTCCCGTGAAATACCACTCTGGCTGTTTCGACGTCTAACCCGGATTCGGGGACAGTGCCTGGTGGGTAGT TTGACTGGGGCGGTTGCCTCCTAAAGGGTAACGGAGGCGCCCAAAGGTCCCCTCAGCCTGGTTGGAAATCAGGCGTTGAGTGTAAGGGCACAAGGGGGCT TAACTGTGAGACCGACGGTGAGCAGATGCGAAAGGGGCCTAGTGATCCGGCGGTGGCGGTGGAAGCGCCGTCGCTCAACGGCTAAAGGTACCCCGGGATA ACAGGCTGATCATCCCCAAGAGTCCATATCGACGGGATGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGTAGGTCCAAGGGTTGGCTG TTCGCCCATAAAGCGGTACGCGAGCTGGGTTTAGAACGTGCGAGACAGTTCGGTCCCTATCCGCTGCGCGCGTAGGAGATTGAGGGGGCTGTTCCTAGTA CGAGAGGACCGGAACGGACGAACTCTGGTGTGCCAGTTGTGCCGCCAGGTCAGGCTGGTTGGCTACGTCGGTGGGATAACCGCTGAAACATCTAAGCGGA AGCCCCCCGAGAGAGGTCTCCCAGGCTCCCAGTAGATGACGGGTGATGGCCGG Aeromonas@hydrophila TGACTAAGGTACATGGTGGATGCCTTGGCAGTCAGGCGATGAAGGACGTACTAACTGCGATAAGCCGTGAGCAGTCGGTAAAGACTTCGACCACGGATTT CCGAATGTCGACATGAGCGACCGGGAGACTGAAACATCTAAGTACCCCGGGAAAAGAAATCAACGAGATTCCCTCAGTAGCGGCGAGCGAACGGGGATTA GCCCTGAGTTAGTGGAACGGTCTGGAAAGCCGGCGTACAGGTGAAGCCCCGTAACAAAAATGAGTGGGCGGGACACGTGACATCCTGTCTGAATATGGGG GGACCATCCTCCAAGGCTAAATACTCTGACTGACCGATAGTGAACAGTACCGTGAGGAAAGGCGAAAAGACCTGAGTGAAAAGACTGAAACCGTGTACGT ACAACAGTGGGAGCCTCGGGTGACTGGTACCTTTTGTATAATGGGTCAGCGACTTACATTTTGTAGCGGGTTAACTAGGGAGCCGTAGGGACCGGTCTTA ACTGGGCGTAGTTGCAAGGTGTAGACCCAAACCGGTGATCTAGCCATGGGCAGTTGAAGGTTGATAACATCAACTGGAGGACCGAACACTAACGTTGCAA AGTTAGGGATGACTGTGCTGGGGGTGAAAGGCCAATCAAACTCGAGATAGCTGGTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGGATACTACTGGGGTA GAGCACTGTTTGGGCTAGGGTTCACTAACCCCATGCAAACTCCGAATACCAGTATCCGGGAGACACACGCGGGTGCTAACGTCCGTCGTGAAGAGGGAAA CAACCCAGACCGCCGGCTAAGTCCCAAAGTTGGTTAAGTGGAAACGATGTGGAAGGCTCAGACAGCTAGGATGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAATAGCTCACTAGTCGAGTCGGCCCGGAAGATGTCGGCTAAACCAGGCACCGAAGCTGCGGATAAGTGGTAGGGGAGCGTTCTGTATCTGCAAGGTG TATCGAGAGTATGCTGGAGATATCAGAAGTGCGAATGTGACGTAAGTAACGAAAGGGGGTGAAAAGCCTCCTCGCCGGAAGACCAAGGTTCCTGTCCAAG TTAATCGGGGCAGGGTGAGTCGACCCCTAAGGTGAGGCCGAACGTAGTCGATGGGAAGCAGGTAATATTCTGCACGGGACGGAGAGGCTAGGTGGCCAGA CGGCTGGCATTCCTTCCAGGAAAAGCATCGTACCAAACCGACACAGGTGGTCGGTAGAGAATACCAAGGCGTTGAGAGAACTCGGGTGAAGGAACTAGGC AAAATAGAACCGTAACTTCGGGAGAAGGTTCGCTCTTTGGGTCGCAGTGACCGATGGTGGACTGTTTATCAAAAACACAGCCTCTGCAAACACGAAAGTG ACGTATAGGGTGTGACACCTGCCCGGTGCCGGAAGGTTAATTGATGGGGTCAAGTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGTGTAACCATGGCCATGCTGTCTCCACCCGAGACTCAGTGAAATCGAATTCGC CGTGAAGATCGGTGTACCCGCGGCTAGACGGAAGACCCCGGAACCTTTACTACAGCTTGGCACTGAACATTGAACCTACATGTGTAGGATAGGTGGGAGG CTTTGAAGGCGTGACGCCAGTTGCGCTGGAGCCTCCTGAAATACCACCCTTGTATGTTTGTGTTCTAACGCAGATTCGCGGACAGTGCCTGGTGGGTAGT TTGACTGGGGCGGTCTCCTCCCAAAGAGTAACGGAGGAGCACGAAGGTTGGCTAATCCTGGTCGGACATCAGGAGGTTAGTGCAATGGCATAAGCCAGCT TAACTGCGAGACGGACAGTGAGCAGGTACGAAAGGGTCATAGTGATCCGGTGGTTCTGATGGAAGGGCCATCGCTCAACGGATAAAGGTACTCCGGGATA ACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGAAGTCGGTCCAAGGGTATGCTG TTCGCCATTAAAGTGGTACGCGAGCTGGGTTCAGAACGTGTGAGACAGTTCGGTCCCTATCTGCCGTGGGCGTTGGATGTTGAAGGGATTGCTCCTAGTA CGAGAGGACCGGAGTGAACGAACTCTGGTGTTCGGGTTGTCACGCCAGTGCATGCCCGGTAGCTAAGTCGGCTCGATAACCGCTGAAACATCTAAGCGGA AGCGACCCGAGAGAGTCATCCCAGGGCCGTTGGAGACCACACGTGATGGTGGG Chlamydia@sp CTATTAAGGCTGCTGGTGGATGCCTAGGCATCAAGGCGATGAAGGACGCGTTTACTGCGAAAAGCTCCGGCGAGCTGGAATAAGCTGGACCCGGAGATAT CCGAATGTCTACATGAGCGACCTGCTGACTGAAACATCTTAGTAAGCAGGGAAAAGAAATCAATGAGATTCCCTAAGTAGCGGCGAGCGAAACGGGATGA GCCCGGATCTAGTCGAATCTTCTGGAAATTGAGCGCACAGGTGAAGCCCCGTAACAAGCCTGAGTGGGCCGGACACGTGAAACCCGGTCTGAATCTGGGG AGACCACTCTCCAAGGCTAAATACTATTGATGACCGATAGTGAACAGTACCGTGAGGAAAGGTGAAAAGACCGGAGTGAAAAGACTGAAACCAGCAGCTT ACAACGGTCGAAGGCCAGGCTAACGGGTGCCTTTTGCATGATGAGCCAGCGAGTTACATTAAATGGCAGGTTAAGACCGGAGCCGAAGCGAGCGGTGTTA AAAGCGCGTAGTCATTTGATGTAGACACAAACCAGTGATCTATCCATGACCAGTTGAAGCAAGGTAACACCTTGTGGAGGACCGAAAGTTGCCGTTGAAA AGGCTTGGATGAGTGTGATAGGGGTGAAAGGCCAATCAAACTCGAGATATCTTGTCTCTTCGAAATAACTTTCGGGTTAGCCTCGAAAATCTACAGGGTA GAGCACTGAATTCACGCGGGCTCGCCAAAGGAAATCAAACTCCGAATACTGTTTTTCGGGAGATAGACGTGGGGGATAAGCTTCATTGTCAAAAGGGGAA CAGCCCAGATCGCCGATTAAGCCCCAAATCATGCTAAGTGATAAGGAAGTGAGTTTCTAAAACAGTTGGAATGTTGCTTAGAGGCAGCCTTTAAAGAGTG CGTAACAGCTCACCAATCGAGAAACTCCCGATAATATCGGCTAAGCATAGAGCCGAAATCGCGGGTTAGCGGTAGGAGAGCGTAGTATGGCAGCAAGATG TACCGTAAGAGCGTTGGAGCGCATACTAGTGATAATGTGGCATAAGTAACGAAAGGAGGTGAAAATCCTCCTCGCCGAAAATCCAAGGTTCCAGGGTAAG CTCGTCTTCCCTGGGTTAGCCGGTCCCTAAGCCGAGGCTGAACGTAGGCGATGGCAAGCAGGTAATATTCTGCGCTTGACGAAGACGTTAAGCACCGGAT TGGTCCGGTGTCCTTCCAAGAAATAAACCGTACCAAACCGACACAGGTGGATGGAATAATATTCTCAGGCGGCGAGAGAACTCTCGTTAAGGAACTCGGC AAATTATCCCCGTAACTTCGGGAGAAGGGGAGCCACTCATGCCGCAGAGAAAGGCCCGGGACTGTTTAACAAAAACACAGCCTATGCAAAGTCGTAAGAC AAGTATATGGTGTGATGCCTGCCCAATGCCAAAAGGTCAAAAGGAGAAGTCAAGTTTGAATTTAAGCCCTGGTGAATGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGTATAACGATCTGGGCACTGTCTCAACGAGAGACTCGGTGAAATTGTAGTAGC AGTGAAGATCTGTTTACCCGCAATAAGACGGAAGACCCCGGAACCTTTACTGTACTCTGATATTGGCTTTTGACTTGTCATGTGTAGGATAACCAGGAGA CATTGAAGTCCCCTCGTCAGGGGGGATGGAGTCACGTGAAATACTGGTCTTGACAAGCCGAAATCTAACGAAAATATTCGGACATTGTCAGACGGGCAGT TTTGCTGGGGCGGTATCCTCCTAAAAGGTAACGGAGGAGTCCAAAGCTTGCCTCATCGTGGTTGGTAATCACGAGTCGAGCGTAAAGGTATAAGGCAAGT TAACTGCGAGACCAACAGTGAGCAGATACGAAAGGGGCTTAGTGATCCGGCGGTGGAAGTGGAATCGCCGTCGCTCAACGGATAAAGGTACTCCGGGATA ACAGGCTTATCGCCACCAAGAGTTCATATCGACGTGGCGTTTGGCACCTCGATGTCGACTCATCGCATCCTGGGGCTGGAGAAGGTCCAAGGGTTTGCTG TTCGCCAATAAAGCGGTACGCGAGTTGGGTTCAAAACGTGTGAGACAGTTTGGTCCCTATCTGTTGTGGGCGTAGGATATTGAGAGGACTGCTTCTAGTA CGAGAGGACCGAAGTGGACGAACAATGGTGTTCCGGTTGTTCTGCCAAGACACGCCGGGTAGCTATGTCGGAAGGATAAGCGTTGAAACATCTAAACGCA AGCCCCCTAAGAAAGGTATCCCAGACTCCATGTAGACCACTGGTGATGGTTGG Wolinella CTTTTAAGGCAGATGGTGGATGCCTTGGGTAGTAGGCGATGAAGGACGTACTAGCTGCGATAAGCTTCGGGGAGTTGCCAAAGACTTGATCCGAAGATTT CCGAATGCCTTAATGGGCGACCTAGTGAGTGAAACATCTCAGTAGCTAGGGAAAAGAAATCAAAGAGATTCCGCTAGTAGCGGCGAGCGAACGCGGAACA GGGCGGATCTAGTAGAATCTTTTGGAAAAAGAGCCTAGAGGTGAAGCCCCGTAATAAGCCAGAGTGGCCAGGACACGAGAAATCCGGGCTGAAGCAGGGG AGACCACTCTCCAACCCTAAATACTCTACTACACCGATAGCGAACAGTACCGTGAGGAAAGGTGAAAAGAGAAAAGTGAAAAGACTGAAACCATCTGCCT ACAACATTCGGAGCCCTGGGTGACGGCTGCCTTTTGCATAATGATCCTGCGAGTTGTGGTATCTGGCGGGTTAAGAAGGTAGCCGTAGCGAGCGGTCTTA ATAGGGCGTAGTCAGATGCTGCAGACCCAAGCTAGTGATCTATCCATGGCCAGTTGAAAGTGAGTAACACTCACCGGAGGACCGAACGTGCCCATTGAAA CGGGCGGGATGAGTGTGATAGGGGTGAAAGGCCAATCAAACTTGTGATAGCTGGTCTCTTCGAAATATATTTAGGTATAGCCTCAAGAGTAATAAGGGTA GAGCTCTGATTGGGCTAGCTGCCCGGAAACCCTGTCAAACTTCGAATACTTACCCTTGGGAGTCAGGCGTGGGTGATAAAATCAATCGTCAAAAGGGGAA CAACCCAGACTACCAAATAAGTCCCAAAGCTACCTGAGTGGAAAAGATGTGAGTTACTCAGACAACCAGGAGGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAACAGCTCACTGGTCTAGTGATTCCTGAAAATATCGGCTAAGGTATGCACCGAATTTGTAGATGAGTGGTAGAAGAGCGTTCTAGTGCGTTAAGGTA TACCGCAAGAGTGCTGGAGCGGCTAGAAGTGAGCATGAGGAATGAGTAGCGAAAAGTGGTGAGAATCCACTTCGCCGTAAATCCAAGGTTCCTACGCTAG CTCGTCATCGTAGGGTTAGTCGGGTCCTAAGTCGAGTCCGAAGGTAGACGATGGCAAATCGGTAATATTCGATACGGGACGCATGGGTTAAACGACCAAA CGGTTGGCGTTCGTGCCAAGAAAAGCCCCGTACCAAACCGACACAGGTGGATAGATGAGTATTCTAAGGCGGTGAAAGAACTCTGGTTAAGGAACTCTGC AAACTAACACCGTAAGTTCGCGATAAGGTGTGCCCCCAGGGTCTCAGCAAAGGTCCCCCGACTGTTTACCAAAAACACAGCCTTTGCCAACTCGTAAGAG AAGTATAAGGTGTGACGCCTGCCCGGTGCTCGAAGGTTAAGAGGATCTGTCAAGTTTGAATTGAAGCCCGAGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGTTAAATACCGACCTGCATGAATGGCGTAACGAGATGGGAGCTGTCTCAACCAGGGATTCAGTGAAATTGTAGTGGA GGTGAAAATCCTCCTACCCGCGGCAAGACGGAAGACCCCGGGACCTTTACTACAGCTTGGCACTGCCGATGGGAGCATTATGCGCAGGATAGGTGGGAGG CTTTGAAATCTTCACTCTGGTGGAGATGGAGCCCCGTGAGATACCACCCTTAATGTTTCTTCTGCTAACTGGCATAGCAGGACAATGCCTGGTGGGTAGT TTGACTGGGGCGGTCGCCTCCTAAAAAGTAACGGAGGCTTGCAAAGGTTGGCTCAGAATGGTTGGAAATCATTCGTTGAGTGTAATGGCATAAGCCAGCC TGACTGCGAGACAAACAGTGAGCAGAGTCGAAAGGGTCATAGTGATCCGGTGGTTCTGGTGGAAGGGCCATCGCTCAAAGGATAAAGGTACCCCGGGATA ACAGGCTGATCTCCCCCAAGAGCTCACATCGACGGGGAGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGGGCTGGAGCAGGTCCAAGGGTATGCTG TTCGCCATTAAAGCGGTACGCGAGCTGGGTTCAGAACGTGTGAGACAGTTCGGTCCCTATCTGCCGTGGGCGTAGGAAATTGAGGAGACTGTCCCTAGTA CGAGAGGACCGGGATGGACATGCACTAGTGTACCAGTTGTTCTGCCAAGACACGCTGGGTAGCTACGCTGGCGTGATAACCGCTGAAACATCTAAGCGGA AGCCGCTCAAGAGAACTTTCCCAGGTCGCAGGAAGACTACTGCTGATGGTTGG Simkania CTATTAAGGCTATTGGTGGATGCCTTGGCATCGAGGCGATGAAGGACGCGCGTACTGCGATAAGCTTCGGGGAGCTGGATAAAGCATGAACCGAAGATTT CCGAATGTTCACATAAGCAACCTGCTGATTGAGACATCTAAGTAGGCAGGGAAAAGAAATCAATGAGATTCCCGTAGTAGCGGCGAGCGAAGTGGGAAGA GCCCGGACTTAGCATAATCATCTGGGAAGTGAGCGTACAGGTGAAGCCCCGTGGCAGACCTGAGTGGGCCGGACACGTGAAACCCGGTCTGAATCTGGGG AGACCACTCTCCAAGGCTAAATACTCTCGATGACCGATAGTGCAAAGTACAGTGATGAAAGGTGAAAAGACCTGAGTGAAAAGACTGAAACCAGTAGCTT ACAACGGTCAGAGGCCAGGCTGATGGGTGCCTTTTGCATGATGAGCCAGCGAGTTAAGTTATACGGCTGGTTAAGTACGGAGCCGGAGTGAGCGGCGTTA ATAGCGCTCAGTCGTATGATTTAGACACAAACCAGTGATCTATCCATGACCAGATGAAGCACGATAACATCGTGTGAAGGTCCGAAAGTGTATGTTGAAA AATACTGGATGAGTGTGATAGGGGTGAAAGGCCAATCAAACTTGAGATATCTTGTCTCTCCGAAATAACTTTAGGGTTAGCCTTGACTTCTTTTGGGGTA GAGCACTGGATTCCCAAGGGCTCGCCAAAGGAAACCAAACTCCGAATACTAATAGTCAGGAGATAGACGTGGGGGATAAGCTTCATTGTCAAAAGGGGAA CAGCCCAGATCGCCGATTAAGCCCCTAATCATGCTAAGTGATAAGGATGTAAGTTTCACAGACAGTTGGAATGTTGCTTAGAGGCAGCCTTTAAAGAGTG CGTAACAGCTCACCAACCGAGAAATTTCCGATAATAACGGCTAAGCATAGAGCCGAAATCGCGGGTTTGCGGTAGGAGAGCGTAGTATGGCGGTAAGATA TACCGAAAGAGTGTTGGAGCGCATACTAGTGAGGATGTGGCATGAGTAACGAAAGGAAGTGAGAATCTTCCTCGCCGAAAGCCTAAGGTTCCAGGGTAAG CTCGTCTTCCCTGGGTTAGCCGGCCCCTAAGCCGAGGCAGAACGTAGGCGATGGAAAGCAGGTAATATTCTGCGCACGACGAAGATGTTAAGCACCGAAT TGGTTCGGTGTCCTTCCAAGAAATATACCGTACCAAACCGACACAGGTAGGCTGATGAATATTCTCAGGCGGCGAGACAACTCTCGTTAAGGAACTCGGC AAATTATCCTCGTAACTTCGGAAGAAGAGGAGCCCCTTGGGCCGCAGAGAAAGGCCCGGGACTGTTTAACAAAAACACAGCCTATGCAAACTCGTAAGAG AAGTATATGGTGTGATGCCTGCCCAATGCCAAAAGGTCAACAGGAGGCGTTCGGGCTGAATATAAGCCCTGGTGAATGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGATCTGGGCGCTGTCTCAACGAGAGACTCGGTGAAATTGTAGTAGC GGTGAAGATCCGTTTACCCGCAGCTAGACGGAAGACCCCGGAACCTTTACTGTACTCTGATATTGGCTTTTGACTTGTCATGTGTAGGATAGCCGGGAGG CTGTGAAAGAGATTCGTCAGGATTTCTGGAGCCTCCTGAAATACCGGCCTTGACATGTTGAAATCTAACGAAGATGTTCGGACATTGTCAGACGGGCAGT TTGACTGGGGCGGTATCCTCCTAAAATGTAACGGAGGAGTTCAAAGCTTGCCTCATCGTGGTTGGCAATCACGATTAGAGCGTAAAGGTATAAGGCAAGT TGACTGCGAGACCAACGGTGAGCAGGTACGAAAGGGACTTAGTGATCCGGCGGTGGAAGTGGAATCGCCGTCGCTTAACGGATAAAGGTACTCCGGGATA ACAGGCTTATCGCCACCAAGAGTTCATATCGACGTGGCGTTTGGCACCTCGATGTCGACTCATCGCATCCTGGGGCTGTAGAAGGTCCAAGGGTTTGCTG TTCGCCAATAAAGCGGTACGCGAGTTGGGTTCAGAACGTGTGAGACAGTTTGGTCCCTATCTGCTGTGGGCGTAGGATATTGAGAAGACTGCTTCTAGTA CGAGAGGACCGAAGTGGACGAACAATGGTGTTCCGGTTGTTCTGCCAAGACATGCCGGGTAGCTATGTCGGAAGGATAAGCGTTGAAACATCTAAACGCA AGCCTCTTAAGAAAAGTATCCCAGACAACCTGAAGACGACGGGTGATGGCTGG Acinetobacter TAATTAAGGCATGTGGTGGATGCCTTGGCAGTCAGGCGATGAAAGACGTAATAGCTGCGATAAGCTCCGGGGAGGCGCAAAATCCTTGATCCGGAGATTT CTGAATGTTGACATAAGCGACGAGGGGAGTGAAACATCTCAGTACCCTTGGAAAAGAAATCAATGAGATTCCCTTAGTAGCGGCGAGCGAACGGGGATCA GCCCTAATTTAGTGGAACGCTCTGGGAATGCGAACTAGAGGTGAATTCCCGTAACAAGTGAGAGTGGGCGAGGCACGTGAAACCTTGTCTGAATATGGGG GGACCATCCTCCAAGGCTAAATACTCTGACTGACCGATAGTGAACAGTACCGTGAGGAAAGGCGAAAAGACCTGAGTGAAAAGTCTGAAACCGCATGCAT ACAACAGTGGGAGCCGTCGGTGACTGGTACCTTTTGTATAATGGGTCAGCGACTTATATTCAGTAGCGGGTTAACTAGGGAGCCGTAGAGATCGGTCTTA ATAGGGCGTAGTTGCTGGGTATAGACCCAAACCGGCGATCTATCCATGAGCAGTTGAAGGTTGGTAACACTAACTGGAGGACCGAACACTGTCGTTGAAA AGCCAGGGATGACTGTGATAGGGGTGAAAGGCTAATCAAGCCTGTGATAGCTGGTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGGATACCATAGGGGTA GAGCACTGTTTCGGCTAGGGTTCACTAAACCGATGCAAACTCCGAATACCTATATCCGGGAGACAGACGCGGGTGCTAACGTCCGTAGTCAAGAGGAAAA CAATCCAGACCGCCAGCTAAGCCCCAAAACTAGTTAAGTGGAAACGATGTGGAAGGCATAGACAGCTAGGAGGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAATAGCTCACTAGTCGAGTCGGCCCGGAAGATGTCGGCTAAACTATGTGCCGAAGCTGCGGATTTGTGGTAGGGGAGCGTTCTGTACCGATAAGGTG TATTGAGAGTATGCTGGAGGTATCAGAAGTGCGAATGTGACGTGAGTAACGAAAACGGGTGAAAAACCCGTTCGCCGAAAGACCAAGGTTCCAGTCCAAG TTAATCGGGGCTGGGTGAGTCGACCCCTAAGGCGAGGCCGAACGTAGTCGATGGGAAATTGGTAATATTCAATACAGGACGGAGAGGTTAAGTCACCTGT TGGCAGGGGCTCCTTCCAGGAAAAGTATCGTACCAAACCGACACAGGTGGTCGGTCGAGTAGACCAAGGCGTTGAGAGAACTCTGCTGAAGGAACTAGGC AAAATGGTACCGTAACTTCGGGAGAAGGTACGCTGTTTGCGCCACAGAAACCGGCCGTGAACTGTTTATTAAAAACATAGCCTCTGCAAACACGAAAGTG ACGTATAGGGTGTGACGCCTGCCCGGTGCCGGAAGGTTAAGTGATGGGGTTAAGTCTTGATCGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCATAATGATGGCGGCGCTGTCTCCAGCAGAGGCTCAGTGAAATCGAAATCGC TGTGAAGATCAGTGTACCCGCGGCTAGACGGAAGACCCCGGAACCTTTACTGCAGCTTGACATTGAACTTTGACCTTACTTGTGTAGGATAGGTGGGAGG CTTTGAAGTTGGAACGCTAGTTCCAATGGAGCCTCCTGAAATACCACCCTGGTAATGTTGGGTTCTAACTCTGATGCGAGGACCATGTCTGGTGGGTAGT TTGACTGGGGCGGTCTCCTCCTAAAGAGTAACGGAGGAGTACGAAGGTGCGCTCAGCGTGGTCGGAAATCACGCGTAGAGTATAAAGGCAAAAGCGCGCT TAACTGCGAGACCCACAGTGAGCAGGTACGAAAGGGTCTTAGTGATCCGGTGGTTCTGATGGAAGGGCCATCGCTCAACGGATAAAGGTACTCTGGGATA ACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGGTTTGGCACCTCGATGTCGGCTCATCTCATCCTGGGGCTGAAGCAGGTCCAAGGGTATGCTG TTCGCCATTAAAGAGGTACGCGAGCTGGGTTTAGAACGTGTGAGACAGTTCGGTCCCTATCTACCGTGGGCGCTGGAAATTGAGAGGACTGCTCCTAGTA CGAGAGGACCAGAGTGGACGAACTCTGGTGTACCGGTTGTGACGCCAGTCCACGCCGGGTAGCTATGTCGGAGGGATAACCGCTGAAACATCTAAGCGGA AGCCTCCTAAGAAAGATTTCCCAGAGCCGTTCGAGACTAGACGTGATGGTTGG Klebsiella CGACTAAGGTACACGGTGGATGCCCTGGCAGTCAGGCGATGAAGGACGTGCTAACTGCGAAAAGCGTCGGTAAGGTGATATAACCTTTAACCGGCGATGT CCGAATGTCGACATGAGCGACCGGGGGACTGAAACATCTAAGTACCCCGGGAAAAGAAATCAACGAGATTCCCCCAGTAGCGGCGAGCGAACGGGGAGCA GCCCAGTGTTAGTGGAACGGTCTGGAAATCCGACGTACAGGTGAAGTCCCGTAACAAAGAAGAGTGGGCGGGACACGTGGTATCCTGTCTGAATATGGGG GGACCATCCTCCAAGGCTAAATACTCTGACTGACCGATAGTGAACAGTACCGTGAGGAAAGGCGAAAAGACCGGAGTGAAAAGACTGAAACCGTGTACGT ACAACAGTGGGAGCACCGTGTGACTGGTACCTTTTGTATAATGGGTCAGCGACTTATATTCTGTAGCAGGTTAACTAGGGAGCCGCAGGGACCGGTCTTA ACTGGGCGAAGTTGCAGGGTATAGACCCAAACCGGTGATCTAGCCATGGGCAGTTGAAGGTTGGTAACACTAACTGGAGGACCGAAGACTAATGTTGAAA AATTACGGATGACTGTGCTGGGGGTGAAAGGCCAATCAAACCGGAGATAGCTGGTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGCATCTTCGGGGTA GAGCACTGTTTCGGCTAGGGTTCACTAACCCGATGCAAACTACGAATACCGATGCACGGGAGACACACGCGGGTGCTAACGTCCGTCGTGAAGAGGGAAA CAACCCAGACCGCCAGCTAAGTCCCAAAGCTGGTTAAGTGGAAACGATGTGGAAGGCACAGACAGCCAGGATGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAATAGCTCACTGGTCGAGTCGGCCCGGAAGATGTCGGCTAAACCATGCACCGAAGCTGCGGCATATGGGTAGGGGAGCGTTCTGTACCTGCAAGGTG TGCTGTGAGCATGCTGGAGGTATCAGAAGTGCGAATGTGACATAAGTAACGAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGTTCCTGTCCAAG TTAATCGGGGCAGGGTGAGTCGACCCCTAAGGCGAGGCCGAACGTAGTCGATGGGAAACAGGTAATATTCTGTACGGGACGGAGAGGCTATGTTACCGGA CGGCCGGAACATCTTCCAGGAAAAGCATCGTACCAAACCGACACAGGTGGTCGGTAGAGAATACCAAGGCGTTGAGATAACTCGGGTGAAGGAACTAGGC AAAATGGTGCCGTAACTTCGGGAGAAGGCACGCTGGTGACGTCGAAGATACCGCTGGTGAACTGTTTATTAAAAACACAGCCTGTGCAAACACGAAAGTG ACGTATACGGTGTGACGCCTGCCCGGTGCCGGAAGGTTAATTGATGGGGTTAAGTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAATGATGGCCAGGCTGTCTCCACCCGAGACTCAGTGAAATTGAACTCGC TGTGAAGATCAGTGTACCCGCGGCAAGACGGAAGACCCCGGAACCTTTACTATAGCTTGACACTGAACATTGAGCCTTGATGTGTAGGATAGGTGGGAGG CTTTGAAGCGTGGACGCCAGTCTGCGTGGAGCCACCTGAAATACCACCCTTTAATGTTTGTGTTCTAACGTTGACTTGCGGACAGTGTCTGGTGGGTAGT TTGACTGGGGCGGTCTCCTCCCAAAGCGTAACGGAGGAGCACGAAGGTTAGCTAATCCTGGTCGGACATCAGGAGGTTAGTGCAATGGCATAAGCTAGCT TGACTGCGAGCGTGACGCGGAGCAGGTGCGAAAGGGTCATAGTGATCCGGTGGTTCTGATGGAAGGGCCATCGCTCAACGGATAAAGGTACTCCGGGATA ACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGAAGTAGGTCCAAGGGTATGCTG TTCGCCATTAAAGTGGTACGCGAGCTGGGTTTAGAACGTGTGAGACAGTTCGGTCCCTATCTGCCGTGGGCGCTGGAGATTGAGGGGGCTGCTCCTAGTA CGAGAGGACCGGAGTGGACGCATACTGGTGTTCGGGTTGTCATGCCAATGCATGCCCGGTAGCTAAATCGGAGAGATAAGTGCTGAAACATCTAAGCACA AACTTCCCGAGAGAGTTCTCCCAGGAACGTTGAAGACGACACGTGATGGCCGG Thermomonospora CTGTCAAGGCACACGGTGGATGCCTTGGCACCAAGCCGATGAAGGACGTGGGAGCTGCGATAAGCCCCGGGGAGCCGCAGCAGGCGAGATCCGGGGATCT CCGAATGTCCACATGAGGGACGCGGCGAGTGAAACATCTCAGTAGCCGCGGAAGAGAAAACAACGTGATTCCCTTAGTAGTGGTGAGCGAACGGGGAACA GGCCGGAGACAGCCGAAGCGCCTGGAACGCCCGGATACAGGTGAACCCCCGTAGCAATCCCAAGTGCACGGGACCCGGGAAAGCTCGTGTGAATCCGCCA GGACCACCTGGTAAGCCTAAATACTCCTGGTGACCGATAGTGAACAGTACCGTGAGGAAAGGTGAAAAGTCCGGTGTGAAAAGACTGAAACCGTGTGCTT ACAACCGTGGGAGCGCCAAGTGACCGGTGCCTTTTGAAGAATGAGCCTGCGAGTTGACGTGCGTGGCAGGTTAACTGGGAAGCCGTAGCGAGCGGTCTGA ACAGGGCGGAGTCGCGCGCGTCAGACCTAAGCCGGTGATCTACCCATGGGCAGGTGAAGCTCAGTAAGACTGGGTGGAGGCCCGAACACCAGGGTTGAAA ACCTGGGGATGACTGTGGTAGGGGTGAAAGGCCAATCAAACTCGTGATAGCCGGTCTCCCCGAAATGCATTTAGGTGCAGCGTCGCGTTCTGCCGAGGTA GAGCACTGGATGGCCGAGGCCCAGGTAACGTCAGCCAAACTCCGAATGCCGGGACGCGGCAGTGAGACGCGGGGGATAAGCTTCGTAGTCGAGAGGGAAA CAGCCCGGACCACCGGCTAAGCCCCCAAGGGTGCTGAGTGGAAAGGATGTGAGTCGCAGTGACAACCAGGAGGTTGCTTAGAAGCAGCCTTGAAAGAGTG CGTAATAGCTCACTGGTCAAGTGATTTCCGACAATGTCGGCTAAGCACACCGCCGAAGCCGTGGCATATGGGTAGGGGAGCGTCGCGCGCGGGTAAGCGG CGGAGTGACCGCCGTGGACGCCACGCGAGTGAGAATGAGGCATGAGTAGCGATGAGGGGTGAGAAACCCCTCCGCCGGATGACCAAGGTTCCTGGGGCAG TTAATCCGCCCAGGGTAAGTCGGGACCTAAGGCGAGGCCGAACGTAGTCGATGGACAACGGGTGATATTCCGTACGTGACGCAGAGGGTAGCCCACCCAG TGGTGGGGGGTCCTGTCGAGAAAAACCCCGTACCAAACCGACGCAGGTGGTCGGTAGAGAATACCCAGGCGTCGGGTGAACCGTGGTCAAGGAACTCGGC AAATTGCCCCCGTAACTTTGGGAGAAGGGGGGCCGGTCACGCCGCAGAGACCGGCCCGGGACTGTTTACTAAAAACACAGGCCGTGCGAAGTCGTAAGAC ATGTATACGGACTGACGCCTGCCCGGTGCCGGAACGTTAAGGGGACGGGTTCGGTCGAAACCTAAGCGCCGGTAAACGGCGGTGGTAACTATAACCATCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGATCTGGGCACTGTCTCGACCGCGGACCCGGCGAAATTGCACTGCG AGTGAAGATCTCGCTACGCGCAGCAGGACGGAAGACCCCGGGACCTTCACTACAGCTTGGCATTGGTGTCTGGAGCGGCTTGTGTAGGATAGGTGGGAGG CTATGAAGCCCGGACGCCAGTTCGGGTGGAGCCCCGTGAAATACCACTCTGGCCGTTTTGATGTCTAACCCGCATTGGGGGACAGTGCCTGGTGGGTAGT TTAACTGGGGCGGTTGCCTCCTAAAGGGTAACGGAGGCGCCCAAAGGTCCCCTCAGCCTGGTTGGCAATCAGGTGTCGAGTGTAAGTGCACAAGGGGGCT TGACTGTGAGACCGACGGTGAGCAGGAGCGAAAGGGGACTAGTGATCCGGCACCGGTGGTGGAAGCGGTGTCGCTCAACGGCTAAAGGTACCCCGGGATA ACAGGCTGATCTTCCCCAAGAGTCCATATCGACGGGAAGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGTAGGTCCAAGGGTTGGCTG TTCGCCCATAAAGCGGTACGCGAGCTGGGTTTAGAACGTGCGAGACAGTTCGGTCCCTATCCGCTGCGCGCGTAGGAGATTGAAGGGACCGTCCCTAGTA CGAGAGGACCGGGACGGACGGACTCTGGTGTGCCAGTTGTGCCGCCAGGTCAGGCTGGTTGGCCACGTCGAAGGGATAACCGCTGAAACATCTAAGCGGA AGCTCCCCGAGAGAGGTCTCCCAGGCCCCCAGTAGACCACGGGTGATGGCCGG Waddlia TTACTAAGGCTGCTGGTGGATGCCTTGGCATCAAGGCGATGAAGGACGCGCGTACTGCGATAATCCTCGGTGAGCTGGAAAAAGCGAGACCCGGGGGATT CCGAATGTCTAAATGAGCGACCTGCCGACTGAGACATCTAAGTAGGTAGGGAAAAGAAATCAAAGAGATTCCCTGAGTAGCGGCGAGCGAAATGGGAAGA GCCCGGATGTAGTCGAACCATCTGGAAATTGGATGCACAGGTGAAGTCCCGTAACAAGCCTGAGTAGGCCGGACACGTGAAACCCGGTCTGAATCTGGGG AGACCACTCTCCAAGGCTAAATACTCTTGATGACCGATAGTGAACAGTACCGTGAGGAAAGGCGAAAAGACCTGAGTGAAAAGACTGAAACCAGCAGCTT ACAACGGTCGGAGGCCAGGCTGACGGGTGCCTTTTGCATGATGAGCCAGCGAGTTAATTTATGTGGCGGGTTAAGAACGAAGCCGAAGCGAGCGGTGTGA ATAGCGCGTAGTCACATGAATTAGACACAAACCAGTGATCTATCCATGGTCAGTTGAAGCAAGGTAACACCTTGTGGAGGACCGAAAGTATACGTTGCAA AGTGTTGGATGAATGTGATAGGGGTGAAAGGCCAATCAAACTTGAGATATCTTGTCTCTCCGAAATAACTTTAGGGTTAGCCTTGAGCTTGTGCGGGGTA GAGCACTGGATCCAATAGGGCTCGCCAACGGGAACCAAACTCCGAATACCGCTGCTCGGGAGATAGACGCGGGGGATAAGCTTCGTAGTCGAGAGGGGAA CAGCCCAGACCGTCATCTAAGCCCCAAATCGTGTTAAGTGATAAGGAAGTAAGTTTCTTAGACAGTTGGTATGTTGCTTAGAGGCAGCCTTTAAAGAGTG CGTAACAGCTCACCAATCGAGAGGCTTCCGATAATAGCGGCTAAACACAGAGCCGAAGGTACGGATAGGTGGTAGGAGAGCGTAGTTAGGCGCCAAGGTG TACCGTAAGAGCGCTGGAGCGCTAACTAGTGAGAATGTGGCATGAGTAACGAAAGGGGGTGAAAATCCCCCTCGCCGAAAATCCAAGGTTCCAGGGTAAG CTCGTCTTCCCTGGGTTAGTCGGTCCCTAAGCTGAGGCTGAACGTAGGCGATGGCAAGCAGGTAATATTCTGCACCTGACGAAGGATAGAAGCATCGGAT TGGTCCGATGTTCTTCCAAGAAATAGACCGTACCAAACCGACACAGGTGGATGGATGAGTATTCTAAGGCGGCGAGATAACCCTCGTTAAGGAACTCGGC AAATTATCCTTGTAACTTCGGGAGAAGAGGAGCCGGTACCGTCGCAGAGAAGGGCCCGGGACTGTTTAGCAAAAACACAGCCTATGCAAACCCGTAAGGG AAGTATATGGTGTGACGCCTGCCCAATGCCAAAAGGTCAAACGGAGATGTTTTGATTGAAGTTAAGCCCTGGTGAATGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGTGTAACGATCTGGGCGCTGTCTCAACGAGGGACTCGGTGAAATTGTAGTAGC AGTGAAGATCTGTTTACCCGCAACAAGACGGAAGACCCCGGAACCTTTACTGTACTCTGATATTGGCTTCTGACTTAACGTGTGTAGGATAGCCGGGAGA CTTTGAAAGTTGCTCGTCAGGGCAGCTGGAGTCTCCTGAAATACCGGTCTCGTTAGGCCGGAGTCTAACGTGAATAGACGGACATTGTCAGACGGGCAGT TTTACTGGGGCGGTATCCTCCTAAAAGGTAACGGAGGAGTCCAAAGCTAACCTCATCGCGGTTGGCAATCGCGAGTGGAGCGTAAAGGTATAAGGTTGGT TAACTGTGAGACCTACAGTGAACAGAAACGAAAGGGGCTTAGTGATCCGGCGGTGGAAGTGGAATCGCCGTCGCTCAACGGATAAAGGTACTCCGGGATA ACAGGCTTATCGCCACCAAGAGTTCATATCGACGTGGCGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGGGCTGGAGAAGGTCCAAGGGTTTGCTG TTCGCCAATAAAGCGGTACGCGAGCTGGGTTCAAAACGTGTGAGACAGTTTGGTCCCTATCTGTTGTGGGCGTAGGATATTGAGAGGACTGTTCCTAGTA CGAGAGGACCGGAATGGACGAACGATGGTGTTCCTGTTGTTCTGCCAAGGCAAGCAGGGTAGCTAAGTCGGAAGGATAAGCGTTGAAACATCTAAACGCA AGCCTCCTAAGAAAGGTATCCCAGACGCCATGTAGACGACTGGTGATGGCTGG Pseudomonas@stutzeri TGAAGAAGGCATACGGTGGATGCCTTGGCAGTCAGGCGATGAAAGACGTGGTAGCTGCGAAAAGCTTCGGGGAGTCGCAAAAGACTTGATCCGGAGATGT CTGAATGTCAACATGAGCGACCAGGGGACTGAAACATCTAAGTACCCTGGGAAAAGAAATCAACGAGATTCCCTTAGTAGTGGCGAGCGAACGGGGATTA GCCCAAGTTTAGCGGAACGCTCTGGAAATGCGGCCTAGTGGTGAAGCCCTGTAGCAAAATCGAGTGGACGGAGCACGAGAAACTTTGTCTGAATATGGGG GGACCATCCTCCAAGGCTAAATACTATGACTGACCGATAGTGAACAGTACCGTGAGGAAAGGCGAAAAGACCGGAGTGAAAAGACTGAAACCGTATGCGT ACAACAGTGGGAGCCTTAGGTGACTGGTACCTTTTGTATAATGGGTCAGCGACTTATTTTCAGTGGCGGCTTAACAAGGGAGGCGTAGCGAGCGGTCTTA ATAGGGCGTAGTCGCTGGGAATAGACCCAAACCGGCGATCTATCCATGGGCAGTTGAAGGTTAGTAACACTGACTGGAGGACCGAAGACTACCGTTGAAA AGTTACGGATGACTGTGATCGGAGTGAAAGGCTAATCAAGCTCGAGATAGCTGGTCTCCTCGAAAGCTATTTAGGTAGCGCCTCGTGCACTGCTGGGGTA GAGCACTGTTTCGGCTAGGGTTCACTAAACCGATGCAAACTCCGAATACCAGTGCACGGGAGACACACGCGGGTGCTAACGTCCGTCGTGAAAAGGGAAA CAACCCAGACCGTCAGCTAAGTCCCAAAACTGGTTAAGTGGAAACGATGTGGAAGGCTTAGACAGCTAGGAGGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAATAGCTCACTAGTCGAGTCGGCCCGGAAGATGTCGGCTAAACCAGGTACCGAAGCTACGGGTCAGCGGTAGAGGAGCGTTCTGTACCTGTAAGGTC AGTTGAGAGCTGGCTGGAGGTATCAGAAGTGCGAATGTGACATGAGTAACGAATGCGAGTGAAAAACTCGCACGCCGAAAGACCAAGGTTCCTGCGCAAG TTAATCGACGCAGGGTGAGTCGGTCCCTAAGGCGAGGCTGAGCGTAGTCGATGGGAAACGGGTAATATTCCGTACGGGACGGAGAGGCTAGGCCACAAGT TGGCTTGGGTTCCTTCCAGGAAAAGCACCGTACCAAACCGACACAGGTGGTTGGTAGAGAATACCAAGGCGTTGAGAGAACTCGGGTGAAGGAACTAGGC AAAATGGCACCGTAACTTCGGGAGAAGGTGCGCCGGTTGCGTCGAAGATACCGGCCGTGGACTGTTTATTAAAAACACAGCCTCTGCAAACACGAAAGTG ACGTATAGGGTGTGACGCCTGCCCGGTGCCGGAAGGTTAATTGATGGGGTCAAGTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGATGGCGGCGCTGTCTCCACCCGAGACTCAGTGAAATTGAAATCGC TGTGAAGATCAGTGTATCCGCGGCTAGACGGAAGACCCCGGAACCTTTACTATAGCTTTGCACTGGACTTTGAATTTGCTTGTGTAGGATAGGTGGGAGG CTTTGAAGCGTGGACGCCAGTTCGCGTGGAGCCACCTGAAATACCACCCTGGCAACTTTGGGTTCTAACTCTGATTCGAGGACAGTGTATGGTGGGTAGT TTGACTGGGGCGGTCTCCTCCTAAAGAGTAACGGAGGAGTACGAAGGTGCGCTCAGACCGGTCGGAAATCGGTCGTAGAGTATAAAGGCAAAAGCGCGCT TGACTGCGAGACAGACAGTGAGCAGGTACGAAAGGGTCTTAGTGATCCGGTGGTTCTGATGGAAGGGCCATCGCTCAACGGATAAAGGTACTCCGGGATA ACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGAAGCCGGTCCAAGGGTATGCTG TTCGCCATTAAAGTGGTACGCGAGCTGGGTTTAGAACGTGTGAGACAGTTCGGTCCCTATCTGCCGTGGACGTTTGAGATTGAGAGGGCTGCTCCTAGTA CGAGAGGACCGGAGTGGACGAACTCTGGTGTTCCGGTTGTCACGCCAGTGCATGCCGGGTAGCTACGTCGGAGAGATAACCGCTGAAACATCTAAGCGGA AACTTCCTAAGAGAGATCTCACAGGGCCGTCGAAGACTACACGTGATGGTTGG Thiobacillus TGAATAAGGCATACGGTGGATGCCTTGGCAGAGAGGCGATGAAGGACGTGGATACTGCGAAAAGCCTCGGGGAGCTGTAAGAAGCTTGATCCGGGGATAT CCGAATGTTGACATAAGCCACGCGGTGACTGAAACATCTCAGTAGCTGCGGAAAAGAAATCAACGAGATTCCCGTAGTAGCGGCGAGCGAACCGGGAGCA GCCTCATCTTAGGAGAACGACCTGGGAAGTTGGCCTAGTGGTGAAGCCCCGTATCAAAGCAAAGTGGGCGGGACACGTGGAATCCTGTCTGAAGATGGGG GGACCATCCTCCAAGGCTAAATACTCTCTCTGACCGATAGTGAACAGTACCGTGAGGAAAGGCGAAAAGAGCGGAGTGAAAAGTCTGAAACCGTATGCCT ACAACAGTGGGAGCCCTGGGTGACTGGTACCTTTTGTATCATGGGTCAGCGACTTACTTTCTGTGGCGGCTTAACAAGGAAGCCGTAGGGACCGGTCTGA ATAGGGCAATGTCGCAGGGAGTAGACCCAAACCGACGATCTATCCATGGTCAGATGAAGGTGGGTAAAACCTACTGGAGGTCCGAACACGCCCGTTGAAA AGGTCGGGATAACTGTGATAGGAGTGAAAGGCTAAACAAGTCCGAGATAGCTGGTCTCCCCGAAAGCTATTGAGGTAGGCCGTCGCGTACCTGCCGGGTA GAGCACTGTTACGGCTAGGGCTAGCTAACCCGTTGCAAACTCCGAATACCGGTACGCGGCAGACAGTCGCGGGTGCTAAGCTCCGTCGTCAAGAGGGATA AACCCCAGACCGCCAGCTAAGTCCCCAAATTGGCTCAGTGGAAACGATGTGGAAGGCCCAGACAGCTAGGAGGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAATAGCTCACTAGTCGAGTCGGCCCGGAAGATTTCGGCTAAGCCATATACCGAAGCTGCGGGTTAGCGGTAGGGGAGCGTTCGGTACCGATAAGGTG TGTTGTGAGCATGCTGGAGGTATCCGAAGTGCGAATGTGACATGAGTAGCGAAAGGGTGTGAAAACCACCCTCGCCGTAAGCCCAAGGTTCCTGCGCAAG TCAATCTGCGCAGGGTGAGTCGGCCCCTAAGGCGAGGCCGAACGTAGCTGATGGGAAATCGGTAATATTCGATACGTGACGGAGAAGGTAGCTCACCGGT TGGTGGGGAGTTCTTCCAGGAAAAGCACCGTACCAAACCGACACAGGTGGGCGGAAGAATATTCCAAGGCGTTGAGAGACCTCGGGTGAAGGAACTCGGC AAATTGACACCGTAACTTCGGAAGAAGGTGTGCCCTCTAGGTCGCAGAGATCGGTGGTGAACTGTTTAACAAAAACACAGGCTCTGCAAAGACGAAAGTC ACGTATAGGGTCTGACGCCTGCCCGGTGCCGGAAGGTTAAGTGAGGGGGTCAAGTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAATGATGGCCACACTGTCTCCACCCGAGACTCAGCGAAGTTGAAGTCGC TGTGAAGATCAGCGTTCCCGTGGCAAGACGGAAGACCCCGGCACCTTTACTACAACTTAGCATGGGACCTTGAGATGATTTGTGTAGGATAGGTGGGAGG CTGTGAAACCGGGACGCTAGTTCTGGTGGAGCCGCCTGAAATACCACCCTGGTGATCTTGGGTTCTAACCTCGATTCAGGGACAGTGTTTGGTGGGTAGT TTGACTGGGGCGGTCTCCTCCCAAAGAGTAACGGAGGAGCACGAAGGTACCCTCAGCGCGGTCGGAAATCGCGCAGTGAGTGCAAAGGCACAAGGGTGCT TGACTGCGAGACAGACAGTGAGCAGGTGCGAAAGGGTCTTAGTGATCCGGTGGTTCTGATGGAAGGGCCATCGCTCAACGGATAAAGGTACGCCGGGATA ACAGGCTGATTCCCCCCAAGAGTTCACATCGACGGGGGGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGGGCTGTAGCCGGTCCAAGGGTATGCTG TTCGCCATTAAAGCGGTACGCGACCTGGGTTCAGAACGTGTGAGACAGTTCGGTCCCTATCTGCCATGGGCGTTGGAGATTGAAGGAACTGCTCCTAGTA CGAGAGGACCGGAGTGGACGTACTCTGGTGTTCCGGTTGTTCTGCCAAGGCATGCCGGGTAGCTATGTCGGCGGGATAACCGCTGAAACATCTAAGCGGA AGCCATCCAAGAGAGATCTCCCAGGGACGTGGAAGACTACACGTGATGGCTCC Thermomonospora@chro TTGTGTAGGCACACGGTGGATGCCTTGGCATCAAGCCGATGAAGGACGTGGGAGCTGCGATAAGCCTCGGGGAGTCGCAGCAGACGTGATCCGGGGATGT CCGAATGTCTTCATGAGGGAGCCGGGGAGTGAAACATCTCAGTACCCGCGGAAGAGAAAACAATGTGATTCCGTGAGTAGTGGTGAGCGAAAGCGGATGA GGCTGGAGGTAGCCGAAGGTTCTGGGAAGGCTGCCTAGACGTGAAGCCGGGTAGTAACCCCGAGTGCACGGGGCTCGAGGAATCCTGTGTGAATCTGCCA GGACCACCTGGTAAGCCTGAATACTTCTGGTGACCGATAGTGGAGAGTACCGTGAGGAAAGGTGAAAAGTCCGGTGTGAAAAGACTGAAACCGTGTGCCT GCAACCGTGGGAGCGTTATGTGACTGGTGCCTTTTGAAGAATGAGCCTGCGAGTTACGGTGTGTGGCGGGTTAACTGGGGAGCCGTAGCGAGCGGTCTGA ATAGGGCGGAGTCGCATGCTGTAGACCCAAGCGGGTGATCTACGCATGGGCAGGTGAAGCTCAGTAAGACTGGGTGGAGGCCCGAACACCAGGGTTGAAA ACCTGGGGATGACTGTTGTAGGGGTGAAAGGCCAATCAAACTCGTGATAGCTGGTCTCCCCGAAATGCATTTGGGTGCAGCGTCGCGTTCTGCCGAGGTA GAGCACTGGATGGCCGAGGCCCAGGTAACGTCAGCCAAACTCCGAATGCCGGGACGCGGCAGTGAGACGCGGGGGATAAGCTTCGTAGTCGAGAGGGAAA CAGCCCGGACCACCGGCTAAGCCCCTAAGGGTGCTGAGTGGAAAGGATGTGAGTCGCAGTGACAACCAGGAGGTTGCTTAGAAGCAGCCTTGAAAGAGTG CGTAATAGCTCACTGGTCAAGTGATTTCCGATAATGTCGGCTAAGCACATCGCCGAAGCCGTGGCATGTGGGTAGGGGAGCGTCGTGCGCGGGTAAGCGG CGGAGTGACCGTCGTGGACGCTGTGCGAGTGAGAATGAGGCATGAGTAGCGATGAGGGGTGGGAAACCCCTCCGCCGGATGACCAAGGTTCCTGGGGCAG TTAATCCGCCCAGGGTAAGTCGGGGCCTAAGGCGAGGCCGAACGTAGTCGATGGATAACGGGTGATATTCCGTACGTGACGCAGAAGGTAGTCCACCCAG TGGTGGGGGATTCTGCCGAGAAAAGCCCCGTACCAAACCGACTCAGGTGGTCAGTAGAGAATACTCAGGCGTCGGGTGAACTGTGGTTAAGGAACTCGGC AAATTGCCCCCGTAACTTCGGGAGAAGGGGGGCCTCTTGGGTCGCAGTGGCCGGGGGAGGACTGTTTACTAAAAACATAGGCCGTGCGAAGTCGTAAGAC ATGTATACGGACTGACGCCTGCCCGGTGCCGGAACGTTAAGGGGACCGCTTTGGTGAGAACTTAAGCGCCGGTAAACGGCGGTGGTAACTATAACCATCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCCCCGCTGTCTCAACCGCAGACCCGGCGAAATTGCACTACG AGTAAAGATCTCGTTTCGCGCAGCAGGACGGAAGACCCCGGGACCTTCACTGCAGCTTGACATTGGTGTCTGGGGCGGCTTGTGTAGGATAGGTGGGAGA CTGTGAAGCCTGGACGCCAGTTCGGGTGGAGTCTCGTGAAATACCACTCTGGTCGTTTTGATGTCTAACCCGCATTGGGGGACAGTGTCTGGTGGGTAGT TTAACTGGGGCGGTTGCCTCCTAAAGGGTAACGGAGGCGCCCAAAGGTCCCCTCAGCCTGGTTGGTAATCAGGTGTTGAGTGTAAGTGCACAAGGGGGCT TGACTGTGAGACCGACGGTGAGCAGGAGCGAAAGGGGACTAGTGATCCGGCACCGGTGGTGGAAGCGGTGTCGCTCAACGGCTAAAGGTACCCCGGGATA ACAGGCTGATCTTCCCCAAGAGTCCATATCGACGGGATGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGTAGGTCCAAGGGTTGGCTG TTCGCCCATAAAGCGGTACGCGAGCTGGGTTTAGAACGTGCGAGACAGTTCGGTCCCTATCCGCTGCGCGCGTAGGAGATTGAGGGGGCTGTCCCTAGTA CGAGAGGACCGGGACGGACGAACTCTGGTGTGCCAGTTGTGCCGCCAGGTCAGGCTGGTTGGCTACGTCGGAGGGATAACCGCTGAAACATCTAAGCGGA AGCTCCCCGAGAGAGGTCTCCCAGGCCCCCAGGAGATGACGGGTGATGGCCGG Salmonella@bongori CGACCAAGGTACACGGTGGATGCCCTGGCAGTCAGGCGATGAAGGACGTGCTAACTGCGAAAAGCGCCGGCGAGGTGATATAACCGTGACCCGGCGATGT CCGAATGTCACCATGAGCGACCGGGGGACTGAAACATCTAAGTACCCCGGGAAAAGAAATCAACGAGATTCCCCCAGTAGCGGCGAGCGAACGGGGAGGA GCCCAGCGTTAGTGGAAGCGTCTGGAAAGCACGCGTACAGGTGAAGCCCCGTAACAAAGATGAGTGGGCGGGACACGTGGTATCCTGTCTGAATATGGGG GGACCATCCTCCAAGGCTAAATACTCTGACTGACCGATAGTGAACAGTACCGTGAGGAAAGGCGAAAAGACCGGAGTGAAAAGACTGAAACCGTGTACGT ACAACAGTGGGAGCACCGTGTGACTGGTACCTTTTGTATAATGGGTCAGCGACTTATATTCTGTAGCAGGTTAACAAGGGAGCCGGAGGGACCGGTCTTA ACTGGGCGAAGTTGCAGGGTATAGACCCAAACCGGTGATCTAGCCATGGGCAGTTGAAGGTTGGTAACACTAACTGGAGGACCGAAGACTAATGTTGAAA AATTACGGATGACTGTGCTGGGGGTGAAAGGCCAATCAAACCGGAGATAGCTGGTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGCATCTCCGGGGTA GAGCACTGTTTCGGCTAGGGCTCGCTAACCCGATGCAAACTGCGAATACCGGTGCACGGGAGACACACGCGGGTGCTAACGTCCGTCGTGAAGAGGGAAA CAACCCAGACCGCCAGCTAAGTCCCAAAGCTGGTTAAGTGGAAACGATGTGGAAGGCCCAGACAGCCAGGATGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAATAGCTCACTGGTCGAGTCGGCCCGGAAGATGTCGGCAAAACCATGCACCGAAGCTGCGGCACATGGGTAGGGGAGCGTTCTGTACCGTTAAGGTG TGCTGTGAGCATGCTGGAGGTATCAGAAGTGCGAATGTGACATAAGTAACGAAAGCGGGTGAAAAGCCCGCTCGCCGGAAGACCAAGGTTCCTGTCCAAG TTAATCGGGGCAGGGTGAGTCGACCCCTAAGGCGAGGCCGAACGTAGTCGATGGGAAACGGGTAATATTCCGTACGGGACGGAGAGGCTATGTTGCCGGA CGGCCGGAACACCTTCCAGGAAAAGCATCGTACCAAACCGACACAGGTGGTCGGTAGAGAATACCAAGGCGTTGAGAGAACTCGGGTGAAGGAACTAGGC AAAATGGTGCCGTAACTTCGGGAGAAGGCACGCTGATTGCGTCGAAGATACCGCTGGTGAACTGTTTATTAAAAACACAGCCTGTGCAAACACGAAAGTG ACGTATACGGTGTGACGCCTGCCCGGTGCCGGAAGGTTAATTGATGGGGTCAAGTCCTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAATGATGGCCAGGCTGTCTCCACCCGAGACTCAGTGAAATTGAACTCGC TGTGAAGATCAGTGTACCCGCGGCAAGACGGAAGACCCCGGAACCTTTACTATAGCTTGACACTGAACACTGGTCCTTGATGTGCAGGATAGGTGGGAGG CTTTGAAGCGTGGACGCCAGTCTGCGTGGAGCCTCCTGAAATACCACCCTTTAATGGCTGTGTTCTAACGTGGAATTGCGGACAGTGTCTGGTGGGTAGT TTGACTGGGGCGGTCTCCTCCCAAAGAGTAACGGAGGAGCACGAAGGTTGGCTAATCCTGGTCGGACATCAGGAGGTTAGTGCAATGGCATAAGCCAGCT TGACTGCGAGCGTGACGCGGAGCAGGTGCGAAAGGGTCATAGTGATCCGGTGGTTCTGATGGAAGGGCCATCGCTCAACGGATAAAGGTACTCCGGGATA ACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGAAGTAGGTCCAAGGGTATGCTG TTCGCCATTAAAGTGGTACGCGAGCTGGGTTTAGAACGTGTGAGACAGTTCGGTCCCTATCTGCCGTGGGCGCTGGAAGTTGAGGGGGCTGCTCCTAGTA CGAGAGGACCGGAGTGGACGCATACTGGTGTTCGGGTTGTCATGCCAATGCATGCCCGGTAGCTAAATCGGAGAGATAAGTGCTGAAACATCTAAGCACA AACTTCCCGAGAGAATCTTCCCAGGAACGTTGAAGACGACAGGTGATGGCCGG Neisseria@meningitid TGAATAAGGCATCAGGTGGATGCCTTGGCGATGAGGCGACGAAGGACGTGTAAGCTGCGAAAAGCGCGGGGGAGCTGCAATAAGCAAGATCCCGCGATGT CCGAATGTCCACATGAGCGACCCGGAGACTGAACCATCTAAGTACCCGGGGAAAAGAAATCAACGAGATTCCGCAAGTAGTGGCGAGCGAACGCGGAGGA GCCTACGGATAGAAGAACAAGCTGGGAACTTGACCTAGTGGTGAAGTCCCGTATCAATGAAAAGTGGGCGGGGCACGTGAAATCCTGTCTGAATATGGGG GGACCATCCTCCAAGGCTAAATACTCTCATCGACCGATAGTGAACAGTACCGTGAGGAAAGGCGAAAAGACCGGAGTGAAAAGACTGAAACCTGATGCAT ACAACAGTGGGAGCGCAGTGTGACTGGTACCTTTTGTATAATGGGTCAACGACTTACATTCAGTAGCGGCTTAACAAGGGAGGCGTAGGGACCGGTCTTA ATAGGGCGGAGTTGCTGGGTGTAGACCCAAACCAGTGATCTATCCATGGCCAGTTGAAGGTGCCTAACAGGTACTGGAGGACCGAACACGCATGTTGCAA AATGCGGGATGAGTGTGATAGGGGTGAAAGGCTAAACAAACTCGAGATAGCTGGTCTCCCCGAAAACTATTTAGGTAGTGCCTCGAGCACTGATGGGGTA AAGCACTGTTATGGCTAGGGTTGACTAACCCATGGCAAACTAAGAATACCATTGCTCGGGAGACAGACGCGGGTGCTAACGTCCGTTGTCAAGAGGGAAA CAACCCAGACCGCCAGCTAAGTCCCAAATAAGATTAAGTGGAAACGAAGTGGAAGGCCCAGACAGCCAGGATGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAATAGCTCACTGGTCGAGTCGTCCCGGAAGATGTCGGCTAAATCTATAACCGAAGCTGCGGATTTATGGTAGGGGAGCGTTCTGTACTGATAAGGTG CATTGTAAGTGTGCTGGAGGTATCAGAAGTGCGAATGTGACATGAGTAGCGAAAGCGGGTGAAAAGCCCGCTCGCCGAAAGCCCAAGGTTCCTGCGCAAG TTCATCGGCGTAGGGTGAGTCGGCCCCTAAGGCGAGGCAGAACGTAGTCGATGGGAAACAGGTAATATTCTGTACGGGACGGAGAGGTTAGGTTGCAAGT TGGCTTGAACCCCTTCCAGGAAAAGCACCGTACCAAACCGACACAGGTGGGCAGGAGAGAATTCTAAGGCGTTGAGAGAACTCAGGAGAAGGAACTCGGC AAATTGATACCGTAACTTCGGGAGAAGGTATGCCCTTTGGGTCGCAGAGAATGGTGGTGGACTGTTTATTAAAAACACAGCCTCTGCTAACACGAAAGTG ACGTATAGGGTGTGACGCCTGCCCGGTGCTGGAAGGTTAATTGAAGATGTAGAGATCGGATCGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCCGCACGAATGGCGTAACGATGGCCACACTGTCTCCTCCTGAGACTCAGCGAAGTTGAAGTGGT TGTGAAGATCAATCTACCCGCTGCTAGACGGAAGACCCCGGAACCTTTACTGTAGCTTTGCATTGGACTTTGAAGTCACTTGTGTAGGATAGGTGGGAGG CTTAGAAGCAGAGACGCCAGTCTCTGTGGAGCCTCCTGAAATACCACCCTGGTGTCTTTGGGTTCTAACCCAGATTCGGGGACCGTGCATGGTAGGCAGT TTGACTGGGGCGGTCTCCTCCCAAAGCGTAACGGAGGAGTTCGAAGGTTACCTAGGTCCGGTCGGAAATCGGACTGATAGTGCAATGGCAAAAGGTAGCT TAACTGCGAGACCGACAGTGAGCAGGTGCGAAAGGGACATAGTGATCCGGTGGTTCTGATGGAAGGGCCATCGCTCAACGGATAAAGGTACTCCGGGATA ACAGGCTGATTCCGCCCAAGAGTTCATATCGACGGCGGGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGTAGTCGGTCCAAGGGTATGCTG TTCGCCATTAAAGTGGTACGTGAGCTGGGTTTAAAACGTGTGAGACAGTTTGGTCCCTATCTGCAGTGGGCGTTGGAAGTTGACGGGGCTGCTCCTAGTA CGAGAGGACCGGAGTGGACGAACTCTGGTGTACCGGTTGTAACGCCAGTTCAAGCCGGGTAGCTAAGTCGGAGAGATAAGCGCTGAAACATCTAAGCGCA AACTCCCTAAGAGAGACTTCCCAGAGTCGTTCGAGACCAGACGTGATGGTGGG Ureaplasma TTACTAAGGCTTATGGTGAATGCCTTGGGACAAAGGCGATGAAGGACGTGCTAACTGCGATAAGCAACGGGTAGCTGATAAAGGCTTAATCCGTTGATCT CCGAATGCTGTCATAGCGAACCTGGTGAGTGAAACATCTCAGTAACCAGGGAAAAGAAAACGAAGTGATTCCCTGTGTAGCGGCGAGCGAAAGGGGAGTA GGCCGGAGATAGTAGAATTGGTTGGGAACCAAATCTAGAGGTGAAATCCCGTAACAATCCTGAGTGGGCGGGACACGTGAAATCCTGTCTGAATCCACCC AGACCATTGGGTAAGCCTAAATACTATTTGTCACCGATAGAGCATAGTACCGTGAGGAACGGTGAAAAGACAGGAGTGAAAAGACTGAAACCATAAGCTT ACAAGTGTTAGAGCACAGTGTGATAGGTGCCTTTTGAAGTATGAGCCAGCGAGTTATTATAGCATGCGGGTTAAAAGAGGAGCCGTAGGGACCGGTCTTA ATAGGGCGTAGTATGTTATAATAGACGCAAACGGGTGATCTATCCATGGGCAGTTGAAGGTGAATAACATTCACTGGAGGACCGAACACTTTCGTTGAAA CGACAGGGATGACTGTGATAGTGGTGAAATTCCAATCGAACTCGTGATAGCTCGTCTCGTCGAAATATTTTTAGGAATAGCGTTAGATGGATATGGGGTA AAGCACTGAATCTATGAGCGCCTGTGAAATAGAATCAAACTCTGAATACCATCCTCTAGCAGTCAGACGTGGGGGATAAGCTTCATTGTCGCGAGGGAAA CAGCCCAGATCATTAACTAAGTCCCTAATAATGCTAAGTGGAAACGATGTGAGTTTCATAAACAGCAAGGATGTTGCTTAGAAGCAGCCTTTAAAGAGTG CGTAACAGCTCACTTGTCGAGAGACTCCGGAAGATGTCGGCTAAGCATATAACCGAAGTTATGGGTATGCGGTAGACGAGTGTTGTATAGGGGCAAGGTA GACTGTGAGACTACTGGACTTTATACAAGTAAGAATGTGGCGTGAGTAACGAATGAGAGTGAGAATCTCTCAAACCGATTGACTAAGGTTCCTGGGCAAG GTCGTCCTCCCAGGGTAAGTCGGATCCTAAGGCGAGGCTGAACGTAGTCGATGGAAAACAGGTAATATTCTGTACGTGACGGAGAGGTTATATGTCCGGT TGGCCGGCATACCTTCCAAGAAAAGCTCCGTACCGAACGAACACACGTGGTCAGGAGAATATCCTAAGGTTGCGAGTTAACTACAGTTAAGGAACTCTGC AAATTAACCCCGTACGTTAGCAATAAGGGGTGCTCGTAGGGCCGCAGTGAATGCGAGGGGACTGTTTAACAAAAACACAGCCTATGCTAAGTCGTAAGAC ATGTATATGGGGTGACACCTGCCCAATGCTGTAAGGTTAAAGAAGAATGTCAAGTTTTAACTGAAGCCCCAGTGAATGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAATTCCGTCCCGCTTGAATGGTGTAACCATCTCTTGACTGTCTCAACTGTAGACTCGGTGAAATCCTGGTGAG GGTGAAGACCCCTCTTGGCGTGATTGGACGGAAGACCCCAGAAGCTTTACTGTAGCTTAATATTGGGAAATTTTATTACTTGTAGAGCATAGGTAGGAGA CTGTGAAGTATACTCGCTAGGGTATATGGAGTCACGTGGAATACTACCCTTGTGATAAGATTCTCTAACCTGCATTGGGGGACAGTGTTAGGTGGGCAGT TTGACTGGGGCGGTCGCCTCCCAAAAGGTAACGGAGGCGCGCAACGGTACCCTCAGCACGGTTGGAAATCGTGTATAGAGTGTAATGGTATAAGGGTGCT TGACTGTGAGACTTACAGTGAACAGGTAGGAAACGGTCATAGTGATCCGGTGGCTCAGATGGAATGGCCATCGCTCAACGGATAAAGCTACTCTGGGATA ACAGGCTGATAGTGCCCAAGAGTTCATATCGACGGCACGTTTGGCACCTCGATGTCGACTCATCTCATCCTGGAGCTGAAGCAGGTTCAAGGGTTCGCTG TTCGCCGATAAAGAGATACGTGAGTTGGGTTCAAACCGTGTGAGACAGGTTGGTCCCTATCTGTCATGCCCGTAGGAAGTTGAGAAGACTGTTCCTAGTA CGAGAGGACCGGAATGGACACACTCTTGTGATCCTGTTGTCGCGCCAGCGCATGCAGGGTAGCAACGTTGGATAGAGAAACGCTGAAACATCTAAGTGTA AACTACTTAAGATAATCTTCCCAGAATCGTTAAAGACTATACGTGATGGTCGG Synechocystis CTACAAAGGCTAACGGTGGATACCTTGGCACACAGGCGAAGAAGGACGTGGTTACGACGAAACGCTTCGGGGAGCTGGAAAAAGCATGATCCGGAGGTGT CCGAATGCTAAAAAAGGCAACCTAGTGACTGAAACATCTTAGTAGCTAGGGAAAAGAAAACAAAGTGATTCTCCAAGTAGCGGCGAGCGAACGGGGAACA GCCTGGAATTAGACGAAGCAGCTGAAAACTGCACCGAGGGGTGAAGTCCTGTATCAAACCCGAGTGGTCGGAGCTCGTGGAATTCCGATTGAATCAGCCG GGACCACCCGGTAAGGCTAAATACTATGTGTGACCGATAGCGTAAAGTACCGCGAGGAAAGGTGAAAAGACCGGAGTGAAAAGAATGAAACCGTTAGCCT ACAACAATGGGAGCTCAGAGTGACCGGTGCCTGTTGAAGAATGAGCCGGCGACTTACAGGTTGTGGCAGGTTAAGTTCGAAGCCAAAGTGAGCGGCCTGA ATAGGGCGTAGTCACAATTTGTAGACCCAACCCGGTGATCTAACCATGGCCAGATGAAGCTTAGTAACACTAAGTGGAGGTCCGAAGACTAATGTTGAAA AATTACGGATGAGTGTGTTAGGGGTGAAATGCCAATCGAACCCGAGCTAGCTGGTCTCCCCGAAATGTGTTTAGGCGCAGCGGTTGTTCACTTGGGGGTA AAGCACTGTTTCGCTGCGCGGGGCTGAAAGTGAGGCAAACTCAGAATACCCAGAACGACCAGTAAGACGTGGGGGATAAGCTTCATCGTCGAAAGGGAAA CAGCCCAGACCACCAGCTAAGTCCCCAAACTCACTAAGTGAAAAGGAGGTGGAGTGCATTGACAACCAGGAGGTTTCCTAGAAGCAGCATTAAAAGAGTG CGTAATAGCTCACTGGTCAAGCGCTCCCCGAAAATGACGGCTAAGTGATGTACCGAAGCTGTGGACATGTGGTAGGGGAGCGTTCTGTAAGGGTAAGCAC TAGCGCAACAGGTGTGGACAGTACAGAAGTGAGAATGCGGCTTGAGTAGCGAATATGGGTGAGAATCCCATACCCCGAAATCCTAAGGTTCCTCCGGAAG CTCGTCCGCGGAGGGTTAGTCAGGACCTAAGGCGAGGCCGAACGTAGTCGATGGACAACCGGCAATATTCGGTACGGGACGGAGAGGCTAGTGCAACTGT TGGCAGTGCATCCTTCCAAGAAAAGCCCTGTACCAAACCGACACAGGTAGGAGGTAGAGAATACTAAGGGGGCGAGGTAACTCTCTCTAAGGAACTCGGC AAAATTACCCCGTAACTTCGGGAGAAGGGGTGCCTCCAGAGTCGCAGTGAATGGCCCGGGACTGTTTACCAAAAACACAGGCTCCGCAAAGTCGTAAGAC CAGTATGGGGGCTGACGCCTGCCCAGTGCCGGAAGGTTAAGGAAGTTGGTTAAGTAGCGACTGAAGCCCCGGTGAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCCGCACGAAAGGCGTAACGATCTGGGCACTGTCTCGGAGAGAGGCTCGGCGAAATAGGATTGTC TGTGAAGATCGGACTCCCTGCACCTGGACAGAAGACCCTAGAAGCTTTACTGTAGCTTGGAATTGGGTTCGGGCTTTGCTTGCGCAGGATAGGTGGGAGA CTATGAAGTTGCTCTTGTGGGAGTAATGGAGTCACGTGAGATACCACTCTGGTGAGGCTAAATTCTAACTTGTATAGAAGGACAATTTCAGGTGGGCAGT TTGACTGGGGCGGTCGCCTCCTAAAAGGTAACGGAGGCGCGCAAAGGTTTCCTCAGGCTGGTTGGAAATCAGCCGAAGAGTGTAAAAGCAGAAGGAAGCT TGACTGTGAGACTGACAGTAAACAGGGACGAAAGGGCTTTAGTGATCCGACGGCACTGGTGGAAGGGCCGTCGCTCAACGGATAAAGTTACTCTAGGATA ACAGGCTGATCTCCGCCAAGAGTTCACATCGACGCGGAGTTTGGCACCTCGATGTCGGCTCATCGCAACCTGGGGCGGTAGTACGTCCAAGGGTTGGCTG TTCGCCCATAAAGCGGTACGTGAGCTGGGTTCAGAACGTGTGAGACAGTTCGGTCCATATCCGGTGTAGGCGTAAGAGTTTGAGAGGAACTTCCTTAGTA CGAGAGGACCGGGAAGTACGCACTCTGGTGTACCTGTTATCGTGCCAACGTACGCAGGGTAGCCAAGTCGGGTGGATAACCGCTGAAACATCTAAGTGGA AGCCCCCTAAGAGAGTACTCTCAGGTCACGGGAAGACTACCGTTGATGGCTCT Peptococcus TAACTAAGGCATGCGGTGAATGCCTAGGCGCCGAGCCGAAGAAGGACGCGGTAACTGCGAAAAGCTACGTTGAGTCGCAAGAGACCTGACACGTAGATAT CCGAATACCTCCATGGGGCACCCGGGGACTGAAACATCTAAGTACCCGGGGAAGAGAAAGAAAATCGATTCCCCCAGTAGCGGCGAGCGAAGCGGGAAGA GCCCGGATTTAGCAGAATGACCTGGGAAGTCAGCCTAGAGGTTAAGCCCTGTAGCAAACCGGAGTCCACGAGGCACGAGGAATCTCGTGGGAAGGCGGGG GGCCCACCCCCCAAGGCTAAATACTCCCGGCGACCGATAGTGAACAGTACCGTGAGGAAAGGTGAAAAGCTCGGAGTGAAAAGACTGAAACCGCATGCTT ACAACAGTCACAGCTCTGAGTAGTGGGTACTTTTTGTAGAACGGACCGGCGAGTTGCGTTAAGAAGCCGGTTAAGAAAGGAGCCATAGCGAGCAGTCTTA ATAGGGCGAAGTTTCTTGGCGCAGACCCAAACCGGTGATCTACCCATGAGCAGTTGAAGCGTTGTAAAACAACGTGGAGGACCGAAAGGTGTCGTTGAAA AGACATGGATGACTGTGGTAGGGGTGAAATTCCAATCGAACCCGAGATAGCTGGTCTCCTCGAAATAGCTTTAGGGCTAGCCTCAAGGACCTACGAGGTA AAGCACTGACTGGATGCGGGCTAGCCAAATCTTATCAAACTCAGAATGCCGTAGCTTGGGAGTCAGACATGGGGGATAAGCTTCATAGTCAAAAGGGAAA GAACCCAGACCGTCGTCTAAGTCCCCAAGTGTGTTAAGTGGAAAGGATGTGAATCGCTCAGACAACCAGGATGTTGCTTAGAAGCAGCCTTAAGAGAGTG CGTAATAGCTCACTGGTCCAGGGGTTCCCGAAAATGTCGGCTAAACACCACACCGAAGACACGGAAATTTGGTAGAGGAGCGATCCATTAGAACAAGCGA GAGCGCAACGCTCGTGGACCCAATGGAAGAGAGAATGCGGTATAAGTAACGAAAAGAGGTGAGAATCCTCTTCGCCGAAAGTCTAAGGTTCCTGGGGAAG CTCGTCCGCCCAGGGTAAGTCGGGACCTAAGGCAAGGCCGAACGTAGTCGATGGGAAACAGGAGAAATTCTGTACGTGACGCAGAGGGTACAGCGCGCCG TTGGGCGCCTGCCTGCCAAGAAAAGCCCCGTACCAAACCGACACAGGTAGACGGTAGAGAATACTAAGGCGGCGAGATAACTCTTGTTAAGGAACTCGGC AAAATGAACCCGTAACTTCGGGAAAAGGGTTGCTCCAAGGGCCGCAGAGAAGGGTCCAGGACTGTTTAGCAAAAACACAGGCATTGCCAAATCGTAAGAT ACGTATAATGGCTGACGCCTGCCCGGTGCTGGAAGGTTAAGGGGAAGAGTCAAGTTTGAACCGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCCGCACGAAAGGCGTAACGATCTGGACGCTGTCTCAACAAGGGACTCGGTGAAATTGAATTACC GGTAAAGATCCGGTTACCTGCGATAGGACAGAAGACCCCAGGAGCTTTACTGCACCCTGATATTGGGTTTCGGTTATTTATGTACAGCATAGGTGGGAGA CAGCGAAGCGAGAGCGCCAGTTTTCGCAGAGTCCCCTGGGATACCACCCTTAAGTGATTGAATTCTAACAAGGATTATTGGACATTGTCAGGCAGGCAGT TTGACTGGGGCGGTCGCCTCCTAAAGAGTAACGGAGGCGCTCAAAGGTTCCCTCAGAACGGATGGAAATCGTTCATAGAGTGTAAAGGCAGAAGGGAGCT TGACTGCGAGAGCAACACTGAGCAGGAAGGAAACGGACTTAGTGATCCGGCGGTTGCGGTGGAAGTGCCGTCGCTCAACGGATAAAGCTACCCTGGGATA ACAGGCTTATCTCCCCCAAGAGTTCACATCGACGGGGAGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGGGCTGTAGTAGGTCCAAGGGTTGGCTG TTCGCCCATAAAGCGGTACGCGAGCTGGGTTCAGAACGTGTGAGACAGTTCGGTCCCTATCCATCGTAGGCGTAGGATATTGAGAGGCCTGACCCTAGTA CGAGAGGACCGGGTTGGACACACGCTGGTTAACCGGTTGTCGTGCCAACGCAAGCCGGGTAGCTAAGTTGGCATGATAAACGCTGAAACATCTAAGCGTA AGCAGCCTAAGAGAGATATCCCAGACCCCAGAGAGACGAATGGTGATGGTCGG Lactococcus TTAATAAGGCGCACGGTGGATGCCTTGGCACTAAGCCGATGAAGGACGTGACTACGACGATATTCTAGGGGGAGCAGTAAGACGCATGATCCCTAGGTCT CCGAATGTTCACATAAGTAACGCAGAGACTGAAACATCTAAGTACCTGCGGAAGAGAAAGTAAAACGATTTCGTAAGTAGCGGCGAGCGAACGCGAAGAA GGGCGGATATAGTCGAATAACCTGGGAAGTTAATCAAGAGGTAAAATCCCGTAACAATCCTGAGTGGGCTGGACACGCGAAATCCAGTTTGAATCCGGGA GGACCATCTCCCAACCCTAAATACTCTTAGTGACCGATAGTGAACAGTACCGTGAGGAAAGGTGAAAAGACCGGAGTGAAAAGACTGAAACCGTGTGCCT ACAAAAGTTCGAGCCCAGGGTGAGAGGTGCCTTTTGTAGAATGAACCGGCGAGTTACGTTATGATGCGGGTTAAGAAAGGAGCCGTAGGGACCGGTCTGA ATAGGGCGTAGTATCATGATGTAGACCCAAACCAGTGACCTATCCATGAGCAGGTGAAGGTGTGTAAGACGCACTGGAGGCCCGAAAGGACACGTTGAAA AGTGTTGGATGACTGTGATAGCGGAGAAATTCCAAACGAACTGGAGATAGCTGGTCTCTCCGAAATAGCTTTAGGGCTAGCGTCGAAAGTTATTGAGGTA GAGCACTGTTTGGGTGAGGTCTTGATAATCTCAGATAAACTCCGAATGCTAACATTCGGCAGTCAGACGCGAGTGCTAAGATCCGTAGTCGAAAGGGAAA CAGCCCAGACCAACAGCTAAGTCCCAAAAAATGTTAAGTGGAAAGGATGTGGGTTGCACAGACAACTAGGATGTTACTCAGAAGCAGCTTTCAAAGAGTG CGTAATAGCTCACTAGTCGAGTGACCCCCGAAAATGTCGGCTAAACATATTACCGAAGCTTTGGATTTATGGTAGGAGAGCGTTCTTAAGCGATAAGGTA TACCGTGAGAGTGCTGGAGCGTTAAGAAGTGAGAATGCGGTATGAGTAGCGCAGATAAGTGAGAATCTTATCCACCGTAAGACTAAGGTTCCAGGGGAAG CTCGTCCGCCCTGGGTTAGTCGGGACCTAAGGCGAGGCCGAACGTAGTCGATGGACAACTGGTGATATTCAGTACGGGACGCAGAGGCTAAGAGACCAGA TGGCTGGCTCTCCTGCCAAGAAAAGCCCCGTACCAAACCGACACAGGTAGTCAGGCGAGTAGCCTCAGGTGTCGAGAGAACTCTCGTTAAGGAACTCGGC AAAATAGCCCCGTAACTTCGGGAGAAGGGGTGCTGGAAGCGCCGCAGTGAATGGCCCAAAACTGTTTATCAAAAACACAGCCTCTGCTAAACCGCAAGGT ATGTATAGGGGGTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGAGTGCTTAAGTATGAATTGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCCGCACGAAAGGCGTAATGATTTGGGCACTGTCTCAACGAGAGACTCGGTGAAATTTTAGTACC TGTGAAGATCAGGTTACCCGCGACAGGACGGAAGACCCCAGGAGCTTTACTGTAGTTTGATATTGAGTACCTGTAAGTCATGTACAGGATAGGTAGGAGC CATTGAAATAGGGACGCTAGTTTCTATTGAGGCTTGTGGGATACTACCCTTGACTTATGGTACTCTAACCCGCATAGGGAGACAGTGTCTGACGGACAGT TTGACTGGGGCGGTCGCCTCCTAAAGAGTAACGGAGGCGCTCAAAGGTTGGCTCAGATTGGTTGGAAATCAATCGTAGAGTGTAAAGGTAAAAGCCAGCT TGACTGCGAGAGCTACACTGAGCAGGTAGGAAACGGACTTAGTGATCCGGTGGTACCGATGGAAGGGCCATCGCTCAACGGATAAAGCTACCCTGGGATA ACAGGCTTATCTCCCCCAAGAGTTCACATCGACGGGGAGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGTAGTCGGTCCAAGGGTTGGCTG TTCGCCCATAAAGCGGCACGCGAGCTGGGTTCAGAACGTGTGAGACAGTTCGGTCCCTATCCGTCGCGGGCGTAGGTAATTGAGAGGACTGTCCTTAGTA CGAGAGGACCGGGATGGACTTACGCTGGTGTACCAGTTGTTCCGCCAGGACAGGCTGGATAGCTATGTGGGAGGGATAAGCGCTGAAACATCTAAGTGCA AGCCCCCTAAGAGAGATTACCCAGAGCCCAGAGAGATGATTGGTGATGGCTGG Tropheryma CATTTAAGGCAAATGGTGGATGCCTTGGTATCTAGCCGAAGAAGGACGTAGCAACTGCGATAAGCCTCGGGAAGCTGTAAGGAGCTTGATCCGAGGATTT CCGAATGCTCATATAGGGGACGTGGGGAGTGAAACATCTCAGTACCCACGGAAGAGAAAGCAATGCGATTCCGTTAGTAGTGGCGAGCGAAACCGGAACA GGCCGGATATAGGTGAATGATTTTGAACGTCAACCAAGAGGTGAAGTCCCGTATCAATCCCAAGTGCACGGGCCCCGTGAAATCCCGTGTGAATCTGTCA AGACCACTTGATAAGCCTAAATACTACAGATAACCGATAGTGGAGAGTACCGTGAGGAAAGGTGAAAAGTCCGGAGTGAAAAGACTGAATCCATTTGCTT ACAACCGTCGGAGCAGTTTGTGACGGGTGCCTTTTGAAGAATGAGCCTGCGAGTTAGGATGTGTGGCGGATTAACTTGGTAGTCGTAGCGAGCGGTCTGA ATAGGGCGTAGTCGCATGTCCTAGACCCAAGCGAGTGATCTATCCATGGCCAGCTGAAGCGAGGTAAGACCTCGTGGAGGGCCGAACACTTAGGTTGAAA ACTGAGGGATGAGTGTGATCGGGGTGAAAGGCCAATCAAACTTGTTATAGCTGGTCTCTCCGAAATGCATTTAGGTGCAGCGTTGCGTTCTGCCGAGGTA GAGCACTGGATGGCCAAGGCCCAGGTAACGTCAGCCAAACTCCGAATGCCGGAGCGCAGCAGTGAGGCGCGGGGGATAAGCTTCGTAGCCGAGAGGGAAA CAACCCAGACCACCAATTAAGTCCCTAAGGGTGCTAAGTGGAAAGGATGTGAGTTGCACAGACAGCCAGGAGGTTGCTTAGAAGCAGCCTTGAAAGAGTG CGTAATAGCTCACTGGTCAAGTGATTCCCGACAATGTCGGCTAAGCACATCACCGAAATTGTGGCATTTGGGTAGGAGAGCGTCGTGTGCGAAAAAGCGG CGATGTAATCGCCGTGGACGCTACACGAGTGAGAATGAGGCATGAGTAGCGAAGGCGGGTGAAAAACCCGCCCCCCGAATAACTAAGGTTCCAGGGCCAG CTAATCCGCCCTGGGTAAGTCGGGACCTAAGGCGAGGCCGAACGTAGTCGATGGACAACGGGTGATATTCCGTACGTGACGCAGAAGGTAGCCAACCGGA TGGCCGGTGGTTCTGACTAGAAAAGCCCCGTACCAAACCGACTCAGGTGGTTGGTAGAGAATACCAAGGGGTCGAGAGAATCGTGGTTAAGGAACTCGGC AAAATGCCTCCGTAACTTCGGGAGAAGGAGGGCCTGTACGGTCACAGAAACCGTGGGAGGACTGTTTATTAAAAACATAGGCTGTGCCAAGTCGTAAGAC ACGTATACAGACTGACGCCTGCCCGGTGCCGGAAGGTTAAGAGGACGGGTTTGGTCGGAATTTAAGCCCCGGTAAACGGCGGTGGTAACTATAACCATCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCCCAACTGTCTCAACCGCGAACTCGGCGAAATTGCACTACG AGTGAAGATCTCGTTACGCGTAGCAGGACGGAAGACCCCGAGACCTTTACTATAGCTTGGTACTGGTACTTGGTGCGGTTTGTGTAGGATAGGTGGGAGA CTGTGAAGCGGGTGCGCCAGCACTCGTGGAGTCTTGTGAAATACCACTCTGATCGCCCCGGTGTCTAACTTAGATTCGAGGACAATGCCTGGTGGGTAGT TTAACTGGGGCGGTTGCCTCCCAAAAGGTAACGGAGGCGCCCAAAGGTTCCCTCAGCCTGGTCGGTAATCAGGTGGCGAGTGTAAGTGCACAAGGGAGCT TGACTGCGAGACTGACGGTGAGCAGGGACGAAAGGGGACTAGTGATCCGGCAGTGGCTGTGGAAGCGCTGTCGCTCAACGGATAAAGGTACCTCGGGATA ACAGGTTGGTCCCTCCCAAGAGTCCATATCGACGGAGGGTTCGACACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGTAGCAGGTCCAAGGGTTGGCTG TTCGCCCATAAAGCGGTACGCGAGCTGGGTTTAGAACGTGTGAGACAGTTCGGTCCCTATCCGCTACGCGCGTCGGAAATTGAGAGGACTGACCCTAGTA CGAGAGGACCGGGTTGGACGAACTCTGGTGTACCAGTTGTCCTGCCAAGGCAGGCTGGTTTGCTACGTCGGACGGATAACCGCTGAAACATCTAAGCGGA AACCGCCTAAGAGAGATTTCCAAGGCTCCCAGTAGAACACGGGTGATGGCTCG Buchnera@aphidicola CAAATAAGGTACATGGTGAATGCCTTGGCAGTCAGGCGAAGAAGGACGTGCTAACTGCGAAAAGCGACGGCAAGCTGATATAAGCCTTAACCGTCGATTT CCGAATGTTAAAATAAGCAACCAAGGGACTGAAACATCTAAGTACCTTGGGAAAAGAAATCAACGAGATTCCCTTAGTAGTGGCGAGCGAAAAGGGAAAA GCCCAACTATAGCAGAATGATTTGGAAATTCAGCGTACAGGTGAAGCCCTGTAGCAATGAAAAGTGAGCGGGACACGAGAAATCCTGTTTGAATATGGGG GGACCATCCTCTAAGGCTAAATACTCTGACTGACCGATAGTGAATAGTACCGTAAGGAAAGGCGAAAAGACCGGAGTGAAAAGACTGAAACCGTGTACGT ACAACAGTGGAAGCATTATGTGACTGGTACCTTTTGTATAATGGGTCAGCGACTTGTACTCTGTAGCAGGTTAACAAGGGAGCCGAAGGGACCGGTCCTA AATAGGCGAAGTTTCAGGGTACAGACCCAAACCGGTGATCTAGCCATGAGCAGTTGAAGGTTGGTAAAACCAACTGGAGGACCGAAGACTGATGTTGAAA AATCACGGATGACTGTGCTAGGGGTGAAAGGCCAATCAAACCGGAGATAGCTGGTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGCATCTACGGGGTA GAGCACTGTTTCGGTTAGGGCTCGCTAATCCGATGCAAACTCCGAATACCGTTGCACGGGAGACACACGCGGGTGCTAACGTTCGTTGTGGAAAGGGAAA CAACCCAGACCGCCAGCTAAGTCCCAAAGCTAGTTAAGTGGAAACGATGTGGAAGGCATAAACAGCCAGGATGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAATAGCTCACTGGTCAAGTCGGCCCGGAAGATGTCGGCTAAATTATGCACCGAAGCTGCGGCATATGGGTAGGGGAGCGTTCTGTACCAATAAGATG TATTGTAAATATGTTGGAGGTATCAGAAGTGCGAATGTGACATGAGTAACGAAAGCAGGTGAAAAACCTGCTCGCCGAAAAACTAAGGTTCCTGTCCAAG TTAATCGGGGCAGGGTGAGCCGACCCCTAAGGCGAGGCTGTACGTAGTCGATGGAAAACAGGTAATATTCTGTGCGGGACGAAGAGGTTAGGTTACCAGA CGGCTGGAACTCCTTCCAAGAAAATCATCGTACCAAACCGACACAGGTAGTTGGTAGAGAATACTAAGGCGTTGAGAGAACCCAGGTGAAGGAACTAGGC AAAATAGTGCCGTAACTTCGGGAGAAGGCACGCTAGTGATGTCGAAGATACCGCTGGTGAACTGTTTATTAAAAACACAGCCTGTGCAAACACGAAAGTG AAGTATACGGTGTGACGCCTGCCCGGTGCCGGAAGGTTAATCGAAGGAGTAAAGTCCAGACTGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAATGATGGCCAGGCTGTCTCCACCTGGGACTCAGTGAAATTGAAATTGC TGTGAAGATCAGTATATCCGCGGCAAGACGGAAGACCCCGGAACCTTTACTATAGCTTGACACTGAATTCTGAATTTTAACGTGTAGGATAGGTGGGAGG CTATGAAGTTAAAACGCTAGTTTTAATGGAGCCAACTGAAATACCACCCTTTACAATTCGTGTTCTAACCTAGATGCAGAGACAGTGTCTGGTGGGTAGT TTGACTGGGGCGGTCTCCTCCCAAAGAGTAACGGAGGAGTACGAAGATTGGCTAATCACGGTCGGACATCGTGAGGTTAGTGCAAAGGCATAAGCCAGTT TGACTGTGAGCGTGATGCGGAGCAGGTGCGAAAGGGTCTTAGTGATCCGGTGGTTCTGATGGAAGGGCCATCGCTCAACGGATAAAGGTACTCCGGGATA ACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGAAGCAGGTCCAAGGGTATGCTG TTCGCCATTAAAGTGGTACGCGAGCTGGGTTTAGAACGTGTGAGACAGTTCGGTCCCTATCTGCCGTGGACGTTGGAAGTTGAGGGGGCTGCTTCTAGTA GCAGAGGACCGAAGTGGACGCATACTGGTGTTCGGGTTGTCATGCCAATGCATGCCCGGTAGCTATATCGGAAAGATAAGTGCTGAACCATATAAGCACA AACTTCCCAAGATAATCTTCCCAGGGACGTTGAAGACTACACGTAATGGCTAG Pirellula CTATTAAGGCGTATGGGGGATGTCTTGGTATCAAGGCGATGAAGGGCGTGGAAGCTGCGATAAGCCTGGGGGAGTTGCAAAGAACGTGATCCCGGGATTC CTGAATGACTACATGTGCTACCCAGAGACTGAAACATCTCAGTACCTGGGGAAGAGAAAGAAAATCGATTTCGTCAGTAGCGGCGAGCGAAAGCGAAATA GCCCGGGGCTAGTTGAACGACATGGAAAGTCGGCCCAGAGGTGAAGCCCGGTAACAAGCCTGAGTGGTTCAGGCACGTGAAACCTGGACTGAATCCACGG GGACCATCCCGTAAGGCTAAATACTCCTGATAACCGATAGCGAACAGTATGGCGATGAAAGATGAGAAGACCTGAGGTATGTGACTGAAACCATACGCTT ACAACGGTCGGAGCCCAGGGTGACGGGTGCCTTTTGCATAATGATCCGGCGAGTTACGGTCTGCGGCAGGTTAAATACGAAGCCAGAGGGACCGGTCTGA ATAGGGCGTAGTCGTAGGCTGTAGACGCAAACCAGTGATCTACCCATGAGCAGTTGAAGCGCGGTTATACCGCGTGGAGGACCGAACACTTGGGTTGAAA ACCGAGGGATGACTGTGGGAGGAGTGAAAGTCTAATCAAACTTGAGATATCTCGTCTCTCCGAAATAGCTTTAGGGCTAGCCTTGAGTACCACCGGGGTA GAGAACTGAATCGATTGGCCCTCGGGATGTCGGACCAAACTCCGAATACCGGGACTCAGGAGTCAGTCACGAGGGATAAGCTTCGTGGTCGAGAGGGAAA CAACCCAGACCGTCTGTTAAGTCCCGAAGAACGCTCAGTCATAAGGAGGTGAATTACTGTGACAACCAGGATGTTGCTTAGAAGCAGCCTTTAAAAAGTG CGTAACAGCTTACTGGTCGAGTAATTCCCGATAATGACGGGTAAGCGTCTCACCGAAGCAGCGGACAAGTGGTAGGAGAGCGCCGATAGCAATAGAGCCG TACCGAAAGAGCGGTGTTGGGCTATCGGGTGATTATGCGGAATGAGTAACGAAAACAGGTGAGAATCCTGTTCGCCGAATACCTAAGGTTCCTGGGGAAG CAATTCCGCCCAGGGTTAGCCGGTGCCTTAGTCGAGGCCGAACGTAGACGATGGATAGCAGGTAATATTCTGCGCGGGACGGCGCCGAAAGGTGACGGGG TGGCCCGCATCACGTCCAAGAAAAGCACCGTACTAAACTGACACAGGTAGGTGGTCGAGTAGACCAAGGCGTCGGGAGAACAGTGGTTAAGGAACTCTGC AAAATGACCCCGTAAGTTCGCGATAAGGGGTGCCCCCAGGGCCACAGAAAATGGCTCTGGACTGTTTATCAAAAACACAGGCCCTGCTAACTCGCAAGAG ATGTATAGGGTCTGACGCCTGCCCGGTGCCGGTAGGTTAAGGAAGAGGGTCAAGTCGCGACCGAAGCCCCGGTAAACGGCGGCCGTAACTATGACGGTCC TAAGGTAGCGAAGTTCCTTGTCGGGTAAGTTCCGACCTGCATGAAAGGCGTAACGACTGGAGCACTGTCTCAATCACTGACCCGGTGAAATTGTAGTTGT GGTGAAGATCCACATACCCGCAGTTAGACGGAAGACCCCGGAACCTTTACTGTAGGCTGATATTGGTCTGAGATATGTTCTGTGTAGGATAGGTGGGAGG CTTTGATCTCGGCGCGCCAGCGTCGGAGGAGCCTCCTGAAATACCACCCTGAATATGTTTAGCTCTAACCCTGATCAGGGAACAGTGTCAGTTGGGCAGT TTGACTGGGGCGGTCTCCTCCCAAAGAGTAACGGAGGAGTGCAATGGTACCCTCAGCCTGGTTGGCCATCAGGCAAAGAGCGCAATGGTAAAAGGGTGCT TGACTGCGAGACTTATCGTGAGCAGGTACGAAAGGGTCATAGTGATCCGGTAGTCCCGATGGAAGGGCTATCGCTCATCAGATAAAGGTACTCCGGGATA ACAGGCTTATCGCATCCGAGCGTCCATAGCGGCGATGCGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGGTGAAGAAGCTCCAAGGGTTCGCTG TTCGCCGATAAAGTGGTACGTGAGCTGGGTTCAGACCGTGTGAGACAGGTCGGTCCCTATCTGCTGTGGGCGTACGAATTTGAGGAGGTCTTCTTTAGTA CGAGAGGATTTGGAAGGACGACCTCTGGTGTCCCAGTTGTCATGCCAGTGCAGGCTGGATAGCTATGGCGGAAGGATAAACGCTGAAACATCTAAGCGTA AGCCCCTCAAGATAGAATTCGTAGTCCCCTGGAAGACGACAGGTGATGGCTGG Mycobacterium@smegma TGTTTAAGGCGCATGGTGGATGCCTTGGCACTGAGCCGATGAAGGACGTAGGAGCTGCGATAAGCCTCGGGGAGCTGCAACGAGCGTGATCCGAGGATGT CCGAATGCCAATATGGGGGACGCGGGGAGTGAAACATCTCAGTACCCGTGGAAGAGAAAACAAAGTGATTCCGTGAGTAGTGGCGAGCGAAAGCGGAGGA GGCTGGAGGTAGCGGAAAGGCTTGGGATGCCTGCCTAGAGGTGAAGCCCGGTAGTAAACCCGAGTGCAGCGGGCCCGTGGAATCTGCTGTGAATCTGCCG GGACCACCCGGTAAGCCTGAATACTTCCAGTGACCGATAGCGGATAGTACCGTGAGGAATGGTGAAAAGTCCGGAGTGAAAAGACTGAAACCGTGCGCTT ACAACCGTCAGAGCCCTGGGTGATGGGTGCCTTTTGAAGAATGAGCCTGCGAGTCAGGACATGTCGCGGGTTAACGGGGTAGCCGCAGCGAGCGGTCTGA ATAGGGCGTAGTGGTGTGTTCTGGACCCAAGCGAGTGATCTACCCATGGCCAGGTGAAGCGCGGTAAGACCGCGTGGAGGCCCGAACACTTAGGTTGAAG ACTGAGGGATGAGTGTGGTAGGGGTGAAAGGCCAATCAAACTCGTGATAGCTGGTCTCCCCGAAATGCATTTAGGTGCAGCGTCGCATTCTGCCGAGGTA GAGCACTGGATGGCCGAGGCCCCGGTAACGTCAGCCAAACTCCGAATGCCGGAGTGCGGCAGTGAGACGCGGGGGATAAGCTCCGTCGTCGAGAGGGAAA CAGCCCAGATCGCCGGCTAAGCCCCTAAGGGTGCTAAGTGGAAAGGATGTCAGTCGCGAAGACAACCAGGAGGTTGCTTAGAAGCAGCCTTGAAAGAGTG CGTAATAGCTCACTGGTCAAGTGATTGCCGATAATGTCGGCTAAGCACACCGCCGAAGCCGCGGCAGTTGGGTAGGGGAGCGTCCTGCACCGGTAAGCCG CCGAGTGACGGTGGTGGAGGGTGTGGGAGTGAGAATGAGGCATGAGTAGCGAAGGCAAGTGAGAACCTTGCCCGCCGAAAGACCAAGGTTCCTGGGCCAG CCAGTCCGCCCAGGGTGAGTCGGGACCTAAGGCGAGGCCGAACGTAGTCGATGGACAACGGGTGATATTCCGTACGTGACGCAGAAGGTAGCCGTCCGGG TGGCCGGCGGTTCTGCCGAGAAAAGCCCCGTACCAAACCAACACAGGTGGTCGGTAGAGAATACTAAGGCGACGAGTGAACTATGGTTAAGGAACTCGGC AAAATGCCCCCGTAACTTCGGGAGAAGGGGGACCCATTGGGTGGCACAAACCGTGAGAGGACTGTTTACTAAAAACACAGGCCGTGCGAAGTCGCAAGAC ATGTATACGGACTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGACCCGTTTTGGGAGAATTTAAGCCCCAGTAAACGGCGGTGGTAACTATAACCATCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCTCAACTGTCTCAACCATAGACTCGGCGAAATTGCACTACG AGTAAAGATCTCGTTACGCGCGGCAGGACGAAAGACCCCGGGACCTTCACTACAACTTGGTATTGGTGCTCGATACGGTTTGTGTAGGATAGGTGGGAGA CTGTGAAGCTCACACGCCACTGTGGGTGGAGTCTTGTGAAATACCACTCTGATCGTATTGGCCTCTAACCTCGATTCAGGGACAGTGCCTGGTGGGTAGT TTAACTGGGGCGGTTGCCTCCTCCAATGTAACGGAGGCGCCCAAAGGTTCCCTCAACCTGGACGGCAATCAGGTGTTGAGTGTAAGTGCACAAGGGAGCT TGACTGCGAGACGGACAGTGAGCAGGGACGAAAGGGGACTAGTGATCCGGCACCTCTGGTGGAAGGGGTGTCGCTCAACGGATAAAGGTACCCCGGGATA ACAGGCTGATCTTCCCCAAGAGTCCATATCGACGGGATGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGCAGGTCCAAGGGTTGGCTG TTCGCCCATAAAGCGGCACGCGAGCTGGGTTTAGAACGTGTGAGACAGTTCGGTCTCTATCCGCCGCGCGCGTCAGAAGTTGAGGAAACTGTCCCTAGTA CGAGAGGACCGGGACGGACGAACTCTGGTATACCAGTTGTCCCACCAGGGCAGGCTGGATAGCCACGTCGGCAGGATAACCGCTGAAACATCTAAGCGGA AACCTTTCAAGACAGGCTTCTCAGGCCCCCCGCAGACCACGGATGATGACCAG Leucothrix TGACTAAGGTATGTGGTGGATGCCTAGGCGATAAGGCGATGAAGGACGTAGTAACTGCGAAAAGCCCCGGTGAGCTGTAAAAAGCTGGACCCGAGGATGT CCGAATGTCGACATGAGCTACCCGGAGACTGAAACATCTAAGTACCCGGGGAACAGAAATCAACGAGATTCCCTTAGTAGCGGCGAGCGAACGGGGACCA GCCCCGGGATAAGAGAACACGTTGGGAACGTGACCGAGTGGTGAAGTCCCGTACTAATGAAGAGTGGTCGGGACACGTGATATCCTGATTGAACATGGGG GGACCATCCTCCAAGGCTAAATACTCTTATCGACCGATAGTGAACAGTACCGTGAGGAAAGGCGAAAAGACCGGAGTGAAAAGACTGAAACCGCATACGT ACAACAGTGGGAGCCTTGGGTGACTGGTACCTTTTGTATAATGGGTCAGCGACTTACTCATCGTGGCAGCTTAAGTAGGTAGGCGTAGGGACCGGTCTTA ATAGGGCGAAGTCGCGGTCAGTAGACCCAAACCAGCGATCTATCCATGGCCAGTTGAAGGTGGGTAACACCTACTGGAGGACCGAACACGTATGTTGAAA AATGCGGGATGAGTGTGATCGGAGTGAAAGGCTAATCAAGCTCGAGATAGCTGGTCTCCTCGAAATCTATTTAGGTAGAGCCTCATGTACTCACGGGGTA GAGCACTGTTATGGCTAGGGGGCCCTAACCCATTGCAAACTCCGAATACCGTTACATGGGAGTCACACGCGGGTGCTAACGTCCGTCGTGGAAAGGGAAA CAACCCAGACCGCCAGCTAAGTCCCAAAATCAGCTCAGTGGAAACGATGTGGAAGGCACAGACAGCCAGGAGGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAATAGCTCACTGGTCGAGTCGGCCCGGAAGATTTCGGCTAAGCTGTATACCGAAGCTGCGGAATTTTGGTAGAGGAGCGTTCTGTACCAATAAGGTG AATCGTAAGTTTGCTGGAGGTATCAGAAGTGCGAATGTGACATAAGTAACGAAGACGGGTGAAAAACCCGTCCGCCGAAAATCCAAGGTTCCTGCGCAAG TTAATCGGCGCAGGGTTAGTCGGCCCCTAAGGCGAGGCAGAACGTAGTCGATGGGAAACAGGTAATATTCTGTACGTGACGGAGAGGCTAGGCTAAACAT TGGTGTAAGTCCCTTCCAGGAAAAACACCGTACTAAACGGACACACGTGGATGGATGAGAATTCCAAGGCGTTGAGAGAACTCTGGTGAAGGAACTAGGC AAAATAGCACCGTAACTTCGGGAGAAGGTGCGCCCCATGGGCCGCAGAGACCGGTGGTGGACTGTTTATCAAAAACACAGCCTCTGCTAACGCGAAAGCG ACGTATAGGGTGTGACGCCTGCCCGGTGCCGGAAGGTTAATTGATGGGGTTCGGTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACGGCCACACTGTCTCCACCAGAGGCTCAGTGAAATTGAAATCGC AGTTAAGATCTGCGTACCCGCGGCTAGACGGAAGACCCCGGCACCTTTACTACAGCTTTGCACTGAACATCGGGCCTACTTGTGTAGGATAGCTGGGAGG CTTTGAAACCGGGACGCTAGTTCCGGTGGAGCCATCTGAAATACCAGCCTGGTAGTTCTGTGTTCTAACCACGATTTTGGGACAGTGTATGGTGGGTAGT TTGACTGGGGCGGTCTCCTCCTAAAGCGTAACGGAGGAGCGCGAAGGTTCACTAATCATGGTCGGAAATCATGAGGTTTGTGCAAAGGCATAAGTGAGCT TGACTGCGAGACAGACAGTGAGCAGGTACGAAAGGGTCTTAGTGATCCGGTGGTTCTGATGGAAGGGCCATCGCTCAACGGATAAAGGTACGCCGGGATA ACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGAAGCGGGTCCAAGGGTATGCTG TTCGCCATTAAAGTGGTACGCGAGCTGGGTTCAGAACGTGTGAGACAGTTCGGTCCCTATCTGCCGTGGGCGTTAGAATTTGAGGAAACTGCTCCTAGTA CGAGAGGACCGGAGTGGACGAACTCTGGTGTACCGGTTGTCACGCCAGTGCAAGCCGGGTAGCTAAGTCGGCAGGATAACCGCTGAAACATCTAAGCGGA AGCCCTTCAAGAGAGTATGCTCAGGGCCGTTGAAGACTACACGTGATGGCACC Streptococcus TTAATAAGGCGCACGGTGGATGCCTTGGCACTAAGCCGATGAAGGACGTGACTACGACGAAATGCTTTGGGGAGTTGTAAGAAACATGATCCAGAGATGT CCGAATGCTCGTTAAGGAAACGCAGTGACTGAAACATCTAAGTAGCTGCGGAAGAGAAAGCAAAGCGATTGCCTTAGTAGCGGCGAGCGAAGCGGCAAGA GGGCGGATATAGAAGAATTACCTGGGAAGTAAGCCAAGAAGTAAAGCCTCGTATCAATCCTGAGTCGGCGAGACACGAGAAATCTCGTTGGAATCTGGGA GGACCATCTCCCAACCCTAAATACTCCTAGTGACCGATAGTGAACAGTACCGTGAGGAAAGGTGAAAAGCCCGGAGTGAAAAGACTGAAACCGTGTGCCT ACAAAAGTTCGAGCCCAGGGTGAGAGGTGCCTTTTGTAGAATGAACCGGCGAGTTACGATATGATGCGGGTTAAGAAAGGAGCCGTAGGGACCGGTCTTA ATAGGGCGTAGTATCATGTCGTAGACCCAAACCTGTGACCTACCCATGAGCAGGTGAAGGTGAGTAAAACTCACTGGAGGCCCGAAAGGGCACGTTGAAA AGTGCTGGATGACTGTGGTAGCGGAGAAATTCCAAACGAACTTGAGATAGCTGGTCTCTCCGAAATAGCTTTAGGGCTAGCGTCGATGTCTCTTGAGGTA GAGCACTGTTTGATTGAGGTCTCGATAATATCAGATAAACTCCGAATGCCAAATATCGGCAGTCAGACGCGAGTGCTAAGATCCGTAGTCGAAAGGGAAA CAGCCCAGACCACCAGCTAAGTCCCAAAAAATGTTAAGTGGAAAGGATGTGGGTTGCACAGACAACTAGGATGTTACTTAGAAGCAGCTTTCAAAGAGTG CGTAATAGCTCACTAGTCGAGTGACCCCCGAAAATGTCGGCTAAACATATTACCGAAGCTGTGGATTTATGGTAGGAGAGCGTTCTATGGTGATAAGGTG TACCGTGAGAGCGCTGGAACGCATAGAAGTGAGAATGCGGTATGAGTAGCGAAGACAGGTGAGAATCCTGTCCACCGTATGACTAAGGTTCCAGGGGAAG CTCGTCCTCCCTGGGTTAGTCGGGACCTAAGGAGAGACCGAATGTATCCGATGGACAACAGGTGATATTCTGTACGGGACGCAGAGGCTAACTAACGTGT TGGCACGTAGTCCTGCCAAGAAAAGCCCCGTACCAAACCGACACAGGTAGTCAGGCGAGTAGCCTCAGGTGGCGAGAGAACTCTCGTTAAGGAACTCGGC AAAATGGCCCCGTAACTTCGGGAGAAGGGGCGCTGGTAGCGCCGCAGTGAATGGCCCAAAACTGTTTATCAAAAACACAGCCTCTGCTAAATCGTAAGAT ATGTATAGGGGGTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGAGCGCTTTAGTGTGAATTGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCCGCACGAAAGGCGTAATGATTTGGGCACTGTCTCAACGAGAGACTCGGTGAAATTTTAGTACC TGTGAAGATCAGGTTACCCGCGACAGGACGGAAGACCCCAGGAGCTTTACTGCAGTTTGATATTGAGTATGTGTACCACATGTACAGGATAGGTAGGAGC CTAAGAAGCCGGGACGCTAGTTTCGGTGGAGGCTTGTGGGATACTACCCTTGTGTTATGGTACTCTAACCCAGATTCGGAGACAGTGTCTGACGGGCAGT TTGACTGGGGCGGTTGCCTCCTAAAAGGTAACGGAGGCGCCCAAAGGTTCCCTCAGAATGGTTGGAAATCATTCGCAGAGTGTAAAGGTATAAGGGAGCT TGACTGCGAGAGCTACACTGAGCAGGGACGAAAGGGGCTTAGTGATCCGGTGGTTCCAATGGAAGGGCCATCGCTCAACGGATAAAGCTACCCTGGGATA ACAGGCTTATCTCCCCCAAGAGTTCACATCGACGGGGAGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGTAGTCGGTCCAAGGGTTGGCTG TTCGCCCATAAAGCGGCACGCGAGCTGGGTTCAGAACGTGTGAGACAGTTCGGTCCCTATCCGTCGCGGGCGTAGGAAATTGAGAGGACTGCTCCTAGTA CGAGAGGACCAGAGTGGACTTACGCTGGTGTACCAGTTGTCTTGCCAAAGCACGCTGGGTAGCTATGTGGGAGGGATAAACGCTGAAACATCTAAGTGTA AGCCCCCTAAGAGAGATTTCCCAGAGCCCTGAGAGATGATAGGTGATGGTTAG Clostridium@botulinu CTACAAAGGCGCATGGTGAATGCCTTGGCATCAAGCCGATGAAGGACGCGATAACTGCGATAAGCTTCGGGTAGACGCACAAGTCAGGATCCGAAGATTT CCGAATGTCGACATGAGTAACCCAGGGACTGAAACATCTAAGTACCTGGGGAAGAGAAAGAAAATCGGTTTTCTTAGTAGCGGCGAGCGAAAGGGAAAGA GCCCGGAGTTAACCGAACCAACTGGAAATTGGACCTAGGGGTAAAGTCCTGTAGTAAACCAGAGTCCACGAGACACGTGAAACCTTGTGGGAAGCAGGGA GGACCACCTCCCAAGGCTAAATACTACTGATGACCGATAGTGAACAGTACCGTGAGGAAAGGTGAAAAGACCGGAGTGAAAAGACTGAAACCATGTGCCT ACAACGATCAAAGCACAGTGTGATGAGTGCTTTTTGTAGAACGAGCCAACGAGTTACGGTATGTAGCAGGTTAAGAAAGGAGCCGAAGGGACCGGTCTTA ATAGGGCGTAGTTGCATGCTGTAGACCCAAACCGGTGACCTATCCATGGCCAGTTGAAGCGAGGTAAAACCTCGTGGAGGACCGAAAGTTGCTGTTGAAA AAGCAGGGATGAGTGTGATAGCGGAGAAATTCCAATCGAACTCGATATAGCTGGTCTCCTCGAAATAGCTTTAGGGCTAGCGTCGGAGTGTACTGGGGTA GAGCACTGAATGGGCTAGGGCTGGCTAAACCTTATCAAACTCCGAATACCAGATTCCGGCAGTCAGACGCGAAAGATAAGTTCCGTAGTCAAAAGGGAAA CAGCCCAGATCGTCAGCTAAGTCCCAAAGGAAGTTAAGTGGAAAGGATGTGGATTTCTAAGACAACTAGGATGTTGCTTAGAAGCAGCCTTAAAAGAGTG CGTAATAGCTCACTAGTCAAGAGATCCCCGAAAATGTCGGCTAAACTTAACACCGAAGCTACGGGTATGCGGTAGAGGAACGTCGTAATGGGCTAAGTCG TACCATAAGAGCGGTGGACTGATTACGAGTGAGAATGTGGCATTAGTAGCGAATGTGGGTGAGAATCCCACAGGCCGAATACCTAAGGTTCCTCAGGAAG TTCGTCCGCTGAGGGTTAGTCGGGACCTAAGCTGAGGCCGAACGTAAGCGATGGACAATCGGTGATATTCGATACGTGACGGAGAGGATAGGATGCTAGT TGGCTAGATCTCCTTCCAAGAAAAGCCCCGTACCAAACCGACACAGGTAGGTAGGAGAGAATCCTAAGGCCGCGGAAGAATTGCAGTTAAGGAACTAGGC AAATTGACCCCGTAACTTCGTGAGAAGGGGTGCCTGAGGAGCCGCAGAGAATGGCACAAAACTGTTTAACAAAAACACAGGCTCTGCTAAAGCGAAAGCT ATGTATAGGGGCTGACGCCTGCCCGGTGCTGGAAGGTTAAGGGGAACACTTAAGTGTGAACTTAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTGGCGAAATTCCTTGTCAGGTAAGTTCTGACCCGCACGAATGGCGTAATGACTTGTGCACTGTCTCAACTGCAAATCCGGCGAAGTTGTAGTGCG AGTGAAGATCTCGCTACCCGCGATTGGACGGAAGACCCCGAGAGCTTTACTGTAGCTTAGCATTGAATTTCGGTATTGTCTGTACAGGATAGGTGGGAGA CTGGGAAATCAGAGCGTCAGCTTTGATGGAGTCTCCTGGGATACCACCCTGATAGTACTGAATTCTAACTGGAATGACAGGACATTGTTAGGTGGGCAGT TTGACTGGGGCGGTCGCCTCCTAAAAAGTAACGGAGGCGCCCAAAGGTTCCCTCAGAACGGTCGGAAATCGTTCGTAGAGTGCAAAGGCATAAGGGAGCC TGACTGCGAGACCTACAGTGAGCAGGGACGAAAGGGGCTTAGTGATCCGGTGGTACCTGTGGGAGGGCCATCGCTCAACGGATAAAGCTACCTCGGGATA ACAGGCTGATCTCCCCCAAGAGTTCACATCGACGGGGAGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGAAGTAGGTCCAAGGGTTGGCTG TTCGCCCATAAAGCGGCACGCGAGCTGGGTTCAGAACGTGTGAGACAGTTCGGTCCCTATCCGTCGCGGGCGCAGGAAATTGAGAAGACTGTCCTTAGTA CGAGAGGACCGGGATGGACCGACTATGGTGTACCAGTTGTTTCGCCAGAACAAGCTGGGTAGCTAAGTGGGCGGGATAAACGCTGAAACATCTAAGCGTA AGCCTCTTAAGAGAGATTTCCCAGACCCCTTGAAGACTACAGGTGATGGTCAG Xylella CGAATAAGGCACATGGTGGATGCCTTGGCGGTCAGGCGATGAAGGACGTGGTAGCTGCGAAAAGTGTCGGGGAGCTGGCAAAAGCTTGATCCGGCAATAT CCGAATGTCTTCATGAGCGACCTGGTGACTGAAATATCTAAGTAACCAGGGAAAAGAAATCAACGAGATTCCCTGAGTAGTGACGAGCGAACGGGGATTA GCCCTAATTTAGGAAAACAATCTGGAAAGTTGGCCTAGGGGTGAAGCCCTGTACCAAGGATGAGTGGACGGGGCACGTGAAACCTTGTCTGAATATGGGG GGTCCATCCTCCAAGGCTAAATACTCTGACCGACCGATAGTGAATAGTACCGTGAGGAAAGGCGAAAAGACCGGAGTGAAAAGACTGAAACCATGTGCGT ACAACAGTAGGAGCCCAAGGTGACTGGTACCTTTTGTATAATGGGTCAGCGACTTACTGTTCGTGGCGGCTTAACTAGGGAGGCGAAGGGACCGGTCTGA TAAGGGCGTAGTCGCGGGCAGTAGACCCAAACCGGTGATCTAGTCATGTCCAGGTGAAGGTGCTTAACAGGTACTGGAGGCCCGAACACTCCCGTTGCAA AGGTAGGGATGAGCGTATTAGGAGTGAAAAGCTAATCGAACCCGAGATAGCTGGTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATATCCTCTCGGGGTA GAGCACTGTTATGGCTAGGGTTGACTGAACCATTGCAAACTCCGAATACCGAGATATGGGAGACACACGCGGGTGCTAACGTCCGTCGTGAAAAGGGAAA CAACCCAGACCCACAGCTAAGTCCCAAATCTAGCTAAGTGGAAACGATGTGAAAGGCATAGACAGCCAGGAGGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAATAGCTCACTGGTCGAGTCGGTCCGGAAGATTTCGGCTAAGCTATGAACCGAAGCTTGGGGTTTGCGGTAGAGGAGCGTTCCGTACCTGTAAGGTG AGTTGAGAGCTTGCTGGAGGTATCGGAAGTGCGAATGTGACATGAGTAACGAATATGGGTGAAAAACCCATACGCCGAAAGCCTAAGGTTCCTGCGCAAG TTAATCGGCGCAGGGTTAGTCGGCCCCTAAGGCGAGGGCGAACGTAGTCGATGGGAAGCAGGTAATATTCTGCACGGGACGGAGAGGCTAGGTGTCCGGT TGGCCGGCACTCCTTCCAGGAAAAGCACCGTACCAAACCGACACAGGTAGGTGGATGAGAATTCTCAGGCGTTGAGAGAACTCGGGTGAAGGAACTAGGC AACATGGCACCGTAACTTCGGGAGAAGGTGCACCCTGTGGGTCGCAGAAACCGGCCGTGGACTGTTTATCAAAAACACAGCCTCTGCAAACACGAAAGTG ACGTATAGGGTGTGACGCCTGCCCGGTGCTGGAAGGTTAATTGATGGGGTAAAGTCTTGATCGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACAGCGGCGCTGTCTCCACCCGAGACTCAGTGAAATTGAAATCGC TGTGAAGATCAGCGTTCCCGTGGCAAGACGGAAGACCCCGGAACCTTTACTATAGCTTTACACTGAACGTTGAGTTCGTCTGTGTAGGATAGGTGGGAGG CTATGAAACCGTGACGCTAGTTGTGGTGGAGCCTCCTGAAATACCACCCTGTCGTGCTTGCGTTCTAACCTAGATTCAGGGACAGTGTATGGTGGGTAGT TTGACTGGGGCGGTCTCCTCCCAAAGAGTAACGGAGGAGCACGAAGGTACGCTCAGCGCGGTCGGACATCGCGCACTGTGTGCAAAGGCATAAGCGTGCT TGACTGCGAGATCGACGATAAGCAGGTACGAAAGGGTCTTAGTGATCCGGTGGTTCTGATGGAAGGGCCATCGCTCAACGGATAAAGGTACTCCGGGATA ACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGTAGTCGGTCCAAGGGTATGCTG TTCGCCATTAAAGTGGTACGCGAGCTGGGTTCAGAACGTGTGAGACAGTTCGGTCCCTATCTGCCATGGGCGTTGGAGATTGAGAGGGCTGCTCCTAGTA CGAGAGGACCGGAGTGGACGAACTCTGGTGTTCCGGTTGTCACGCCAGTGCATGCCGGGTAGCTATGTCGGAGCGATAACCGCTGAAACATCTAAGCGGA AGCGCCCTAAGAGAGATCTCCCAGGAACCATGTAGACTACTGGTGATGGTCAG Agrobacterium@vitis TGCGTAAGGCATTTGGTGGATGCCTTGGCATGCAGGCGATGAAGGACGTGATACCTGCGATAAGCCGTGGGGAGCTGCGAAGAGCTTGATCCATGGATTT CCGAATGTCTACATGAGCGACTCGGGGACTGAAACATCTAAGTACCCGAGGAAAGGACATCAACGAGACTCCGTAAGTAGTGGCGAGCGAACACGGACCA GGCCGCATAAAGCGGAACAAGTTGGAAACTTGGCCTAGTGGTGAAGCCCCGTAGCAGACCTGAGTGGGCGGGACACGTGAAATCCTGTTCGAACATGGGG AGACCACTCTCCAAGCCTAAGTACTCTGCATGACCGATAGCGAAAAGTACCGTGAGGAAAGGTGAAAAGCCCGGAGTGAAAAGACTGAAACCGGATGCCT ACAACAGTAGGAGGGCAGCCTGACTGGTACCTTTTGTATAATGGGTCAACGACTTAGTGTAACTAGCAGCTTAAGGTGGTAGGCGCAGCGAGCGGTGTTA ATAGCGCGGAGTTAGTTGCATTAGACCCAAACCAGTGATCTAGCCATGAGCAGTTGAAGGTTGGTAACACCAACTGGAGGACCGAACGCATCTGTTGCAA TAGATGGGATGACTGTGTTAGGGGTGAAAGGCCAATCAAACTCGAAATAGCTGGTCTCCGCGAAAACTATTTAGGTAGTGCGTCGATTACCTCAGGGGTA GAGCACTGGATGGGCTAGGGACCTCTAATCCTAACCAAACTCCGAATACCTGTAATCGGCAGACACACGCGGGTGCTAACGTCCGTCGTGAAGAGGGCAA CAACCCTGACCTCCAGCTAAGTCCCCAAGCTGGCTAAGTGGAAAGGATGTAGGATCCCAAAACAACCAGGATGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAACAGCTCACTGGTCTAGGGTCTTCCGAAAATGTCGGCTAAGCCATGCACCGAAGCTGAGGATTAGTGGTAGCGGAGCGTTCCGTACCTGTAAGGGC AGTCGTGAACATCCTGGAGGTATCGGAAGTGCGAATGTGACATGAGTAACGAAAGGGGGTGAGAGACCCCCTCGCCGAAAGACCAAGGTTCCTGCTTAAG TTAATCTGAGCAGGGTTAGCCGGCCCCTAAGGCGAGGCAGAACGTAGTCGATGGGAACCACGTAATATTGTGGGCGTGACGGATCACACAATTGTCAGTA CTGATTGCAGTGGTTCCAGGAAATACACCGTACCAAACCGACACAGGTGGTCGGTAGAGTATACCAAGGCGTTGAGAGAACTATGTTGAAGGAACTCGGC AAATTGCACGCGTAACTTCGGAAGAAGCGTGACCCCCAAGGTGGCACAGACCGGGGGAGGACTGTTTATCAAAAACACAGGCTCTGCGAAGTCGCAAGAC ACGTATAGGGTCTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGAGAGGTCAAGTTTGAATCGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCCCCGCTGTCTCCAACATAGACTCAGTGAAATTGAATTCCC CGTGAAGATCGGGGTTCCTGCGGTCAGACGGAAGACCCCGGCACCTTTACTATAGCTTTACACTGGCATTCGTGTCGGCATGTGTAGGATAGGTGGTAGG CTTTGAAGCTTGGACGCCAGTTCGAGTGGAGCCTCCTGAAATACCACCCTTATCGTCATGATGTCTAACCGCGATTCCGGGACAGTGTATGGTGGGTAGT TTGACTGGGGCGGTCGCCTCCGAAAGAGTAACGGAGGCGCGCGATGGTGGGCTCAGACCGGTCGGAAATCGGTCGTCGAGTGCAATGGCATAAGCCCGCC TGACTGCGAGACTGACAGTGAGCAGAGACGAAAGGGTCATAGTGATCCGGTGGTCCCGGTGGAAGGGCCATCGCTCAACGGATAAAGGTACGCCGGGATA ACAGGCTGATGACCCCCAAGAGTCCATATCGACGGGGTGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGGGCTGGAGCAGGTCCAAGGGTTTGCTG TTCGCCAATAAAGCGGTACGTGAGCTGGGTTCAGAACGTGTGAGACAGTTCGGTCCCTATCTGCCGTGGGTGTAGGAATTTGACAGGACTGTCCCTAGTA CGAGAGGACCGGGATGGACATATTCTGGTGGACCTGTTGTCGTGCCAACGCAAGCAGGGTAGCTATATTGGATGGATAACCGCTGAAGCATCTAAGCGGA AACCACCTAAAAGAGTATTCCCAGAGCCGTGGAAGACGACACGTGATGGACGG Leptospira TAAGAAAGGCGTACGGGGGATGCCCGGGCATCAACGCGATGAAGGACGTGGCTTCTGCGATAAGCAACGGGGAGTTGTAAGAAGCATGATCCGTTGATTT CCGAATGCGCAAACCGGCAAGTCGGGGATTGAAACATCTTAGTACCCGGATAAAAGAAAATAAGATGATTCCGTCAGTAGCGGTGAGCGAACGCGGAAGA GCCTGGAATTAGCAGAACGGTATGGAAAGCCGACCTAGAGGTGAAGTCCTGTAGCAAACCTGAGTCCACGGAACACGTGTAATTCAGTGGGAATCTGCGG GGACCACCCCGTAAGGCTAAACAGTACTGATGACCGATAGAGAAAAGTACCGCGAGGAAAGGTGAAAAGTGGGGAGTGAAAAGACTGAAACCGTATGCTT ACAAGTATCAGAGCCTTGGGTGATGGGTGCCTTTTGTAGAATGAGCCGGCGAGTTATTTTACGTTGCAGCTTAAGGACGTAGGCGAAGCGAGCGGTCTGA ATAGGGCGAAGTAGCGTGGAATAGACCCAAGCCGTCGAGCTATCCATGTCCAGTTGAAGGTGGGTAAAACTCACTGGAGGACCGAACTTTTTCGTTGAAA AGAATGGGATGAGTGTGATAGGGGTGAAAGGCCTATCAAGGCAGCGATAGCTGGTCTCTCCGAAATAGGTTTAGGCCTAGCGTCAGTTAGTTGCGGGGTA GAGCTCTGAAAGGACTAGGGCCCGCTAAACCCTATCAAACTTCGAATACCGTTCACTGGCAGTCAGACACGGGGGATAAGCTCCGTGGTCAAAAGGGAAA CAGCCCAGACCGTCGTTTAAGCCCCAAAGTATGCTAAGTGGAAAGGATGTGGGGCGCATATACAACCAGGAGGTTGCTTAGAAGCAGCCTTTAAAGAGTG CGTAATAGCTCACTGGTCGAGTGCTCCCCGAAAATGTTCGACAAGCATGGCGCCGAAGGCACGGATTAGTGGTAGGAGAGCGTTCTTTCCCGTTAAGGCG TACCGTAAGAGCGCTGGAGGAGTAAGAAATGAAGATGTGGCATGAGTAGCGTAGGGGAGTGAGATTCTTCCCCACCGATAGCCTAAGGTTCCCCGGGAAG CCAATCCGCCGGGGGTTAGTCGGCCCCTAAGACGAGGCTAGACGTAGTCGATGGGAAGCAGGTCATATTCTGCACGTGACGCAGAGGATAGTTAGGCGGT TGGTTGCTTTCCCTGCCAAGAAATACACCGTACCAAACCGACACAGGTAGGCAGTAGAGAATACTAAGGTGTCGAGATAACTCTCGTTAAGGAACTCGGC AAATTACTCCTGTAACTTCGGGATAAGGGAGACCGGTGGAGTGGCACAAAAAGGGGGAGGACTGTTTACCAAAAACACAGGCTCTGCCAAATCGGAAGAT AAGTATAGGGTCTGACACCTGCCCGGTGCTGGAAGGTCAAGAGGACGGGTCAAGTCGGAATTTAAGCCCCAGTAAACGGCGGCCGTAACTATGACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGTGTAACGACTTCCCCACTGTCTCAACGAGAGTCTCGGCGAAATTGTAGTACC CGTGAAGATCGGGTTACCTGCGATAGGACGGAAGACCCCGGAACCTTTACTGTAACCTGGCATTGAACTTTGGTCCTGTATGTGTAGGATAGGTGGGAGG CTATGAAATCTGGACGCCAGTCTGGATGGAGCCTCGTGAAATACCACCCTTACTTGACCCAGTTCTAACCGAACATTCGAGACAATGTCAGGCGGGCAGT TTGACTGGGGCGGTCGCCTCCTAAAGAGTAACGGAGGCGCCCAAAGGTTCCCTCAGCGCGGACGGAAATCGCGCCAAGAGTGTAAAGGCATAAGGGAGCT TAACTGTGAGACAGACAGTGAGCAGGTACGAAAGGGGCTTAGTGATCCGGTGGTTCTGGTGGAAGGGCCATCGCTCAACGGATAAAGGTACTCCGGGATA ACAGGCTGATCGCGTCCAAGAGTCCATATCGACGACGCGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGAAGCAGGTCCAAGGGTATGCTG TTCGCCATTAAAGCGGTACGCGAGCTGGGTTCAGAACGTGTGAGACAGTTCGGTCCCTATCCATCGCAGGCGTTGGAGATTGACGGAACTGTCCCTAGTA CGAGAGGACCGGGATGGACGAACTCTGGTGTATCAGTTGTTTCGCCAGAACACGCTGAGTAGCTATGTCGGAGGGATAACCGCTGAAACATATAAGTGGA AACCCTCTAAGAAAGATCTCCCAGACCCCAAGAAGATGACTGGTGATGGTCAC Citrobacter CGACTAAGGTACACGGTGGATGCCCTGGCAGTCAGGCGATGAAGGACGTGCTAACTGCGATAAGCGTCGGTAAGGTGATATAACCTTTAACCGGCGATTT CCGAATGTCAACATGAGCGACCGGGGGACTGAAACATCTAAGTACCCCGGGAAAAGAAATCAACGAGATTCCCCCAGTAGCGGCGAGCGAACGGGGAGCA GCCCAGTGTTAGTGGAACGGTCTGGAAATCCGACGTACAGGTGAAGTCCCGTAACAAAGAAGAGTGGGCGGGACACGTGGTATCCTGTCTGAATATGGGG GGACCATCCTCCAAGGCTAAATACTCTGACTGACCGATAGTGAACAGTACCGTGAGGAAAGGCGAAAAGACCGGAGTGAAAAGACTGAAACCGTGTACGT ACAACAGTGGGAGCCTTAGGTGACTGGTACCTTTTGTATAATGGGTCAGCGACTTATATTCTGTAGCAGGTTAACAAGGGAGCCGAAGGGACCGGTCTTA ACTGGGCGAAGTTGCAGGGTATAGACCCAAACCGGTGATCTAGCCATGGGCAGTTGAAGGTTGGTAACACTAACTGGAGGACCGAAGACTAATGTTGAAA AATTACGGATGACTGTGCTGGGGGTGAAAGGCCAATCAAACCGGAGATAGCTGGTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGCATCTTCGGGGTA GAGCACTGTTTCGGCTAGGGTTCACTAACCCGATGCAAACTGCGAATACCGATGCACGGGAGACACACGCGGGTGCTAACGTCCGTCGTGAAGAGGGAAA CAACCCAGACCGCCAGCTAAGTCCCAAAGCCAGTTAAGTGGAAACGATGTGGAAGGCACAGACAGCCAGGATGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAATAGCTCACTGGTCGAGTCGGCCCGGAAGATGTCGGCTAAACTGTGCACCGAAGCTGCGGCATATGGGTAGGGGAGCGTTCTGTACCGTTAAGGTG TGCTGTGAGCATGCTGGAGGTATCAGAAGTGCGAATGTGACATAAGTAACGAATGCGGGTGAAAAACCCGCACGCCGGAAGACCAAGGTTCCTGTCCAAG TTAATCGGGGCAGGGTGAGTCGACCCCTAAGGCGAGGCCGAACGTAGTCGATGGGAAACAGGTAATATTCTGTACGGGACGGAGAGGCTATGTTACCGGA CGGCCGGAACACCTTCCAGGAAAAGCATCGTACCAAACCGACACAGGTGGTCGGTAGAGAATACCAAGGCGTTGAGAGAACTCGGGTGAAGGAACTAGGC AAAATGGTGCCGTAACTTCGGGAGAAGGCACGCTGATTACGTCGAAGATACCGCTGGTGAACTGTTTATTAAAAACACAGCCTGTGCAAACACGAAAGTG ACGTATACGGTGTGACGCCTGCCCGGTGCCGGAAGGTTAATTGATGGGGTTAAGTCTTGATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAATGATGGCCAGGCTGTCTCCACCCGAGACTCAGTGAAATTGAACTCGC TGTGAAGATCAGTGTACCCGCGGCAAGACGGAAGACCCCGGAACCTTTACTATAGCTTGACACTGAACACTGGTCCTTGATGTGTAGGATAGGTGGGAGG CTTTGAAGTGTGGACGCCAGTCTGCATGGAGCCACCTGAAATACCACCCTTTAATGGCTGTGTTCTAACGTGGACTTGCGGACAGTGTCTGGTGGGTAGT TTGACTGGGGCGGTCTCCTCCTAAAGAGTAACGGAGGAGCACGAAGGTTAGCTAATCCTGGTCGGACATCAGGAGGTTAGTGCAAAGGCATAAGCTAGCT TGACTGCGAGAGTGACGCTGAGCAGGTGCGAAAGGGTCTTAGTGATCCGGTGGTTCTGATGGAAGGGCCATCGCTCAACGGATAAAGGTACTCCGGGATA ACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGAAGTAGGTCCAAGGGTATGCTG TTCGCCATTAAAGTGGTACGCGAGCTGGGTTTAGAACGTGTGAGACAGTTCGGTCCCTATCTGCCGTGGGCGCTGGAGATTGAGGGGGCTGCTCCTAGTA CGAGAGGACCGGAGTGGACGCATACTGGTGTTCGGGTTGTCATGCCAATGCATGCCCGGTAGCTAAATCGGAGAGATAAGTGCTGAAACATCTAAGCACA AACTTCCCGAGAGAGTTCTCCCAGGAACGTTGAAGACGACACGTGATGGTCGG Rhodospirillum CAGAGAAGGCATCTGGTGGATGCCTTGGCGTCAAGGCGATGAAGGACGTGGCACCTGCGAAAAGCCATGGGGAGCTGAGAGAAGCTTGATCCATGGATAT CCGAATGTCCCCATGAGCGACCCGGCGACTGAAACATCTAAGTAGCCGGGGAAAGGAAATCAACGAGACTCCGTTAGTAGTGGCGAGCGAACGCGGATCA GCCCGTATAAACCGGAACCGTCTGGAAATCGGGCCTAGCGGTGAAGCCCCGTAGGAGACCTGAGTGGGCGGGACACGTGAAATCCTGTCTGAACGTGGGG GGACCACCCTCCAAGGCTAAGTACTCTTGACGACCGATAGTGCACAGTACCGTGAGGAAAGGTGAAAAGCCCGGAGTGAAAAGTCTGAAACCGGATGCCT ACAACAGTCGGAGCCTCAGGTGACGGGTACCTTTTGTATAATGGGTCAGCGACTTAATCTGGCGAGCAGCTTAAGATGGTAGGCGCAGCGAGCGGTCTTA ATAGGGCGGAGTTCGTCGGATTAGACCCAAACCGGTGATCTAGCCATGGGCAGTTGAAGGTGGATAACACCCACTGGAGGACCGAACACGTCTGTTGAAA AAGACGGGATGACTGTGCTAGGGGTGAAAGGCCAATCAAACTCGAAATAGCTGGTCTCCGCGAAAGCTATTTAGGTAGCGCGTCGGATACCACCGGGGTA GAGCACTGGATGGGCTAGGGCCAGCCAAACCTAACCAAACTCCGAATACCGGTATCCGGCAGACAGACCAGGGTGCTAACGTCCTGGGTCAAGAGGGAAA CAACCCAGACCACCAGCTAAGTCCCCAAGCCGGCTAAGTGGAAAGGATGTGGACGGCCATAACAACCAGGAGGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAACAGCTCACTGGTCTAGCTATCCCCGAAGATGTCGGCTAAGCCGTGCACCGAAGCTGTGGATTCGTGGTAGCGGAGCGTTCCGTACCTGTAAGGTG TCTCGTAAGGATGCTGGAGGTATCGGAAGCGAGAATGTGACATGAGTAGCGAAGGAGTGTGAGAAACACTCCCGCCGAAAGCCCAAGGTTCCTGCGCAAG CTAATCCGCGCAGGGTGAGTCGGCCCCTAAGTCGAGGGCGAACGTAGACGATGGGAATCAGGTAATATTCTGAACGTGACGCCTTTCGGAGTTGTCCTCA TCGGAGGCAGGAAGGCCGGGAAATACACCGTACCAAACCGACACAGGTGGGCGGTAGAGTATACCAAGGCGTTGAGAGAATGGTGTTGAAGGAACTAGGC AAATTGCCCCCGTAACTTCGGGAGAAGGGGGCCCTCCATGGGGGCACAGACCGGGGGGGGACTGTTTACTAAAAACACAGGCTCTGCGAAGTCGCAAGAC ACGTATAGGGTCTGACGCCTGCCCGGTGCCGGAAGGTTAAGAGGAGAGGTCAAGTTTGAATCGAAGCCCCGGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCCCCGCTGTCTCCAACACCAACTCAGCGAAATTGAATTCTC CGTGAAGATCGGAGTTCCCACGGCCAGACGGAAGACCCCAGAACCTTTACTACAACTTCGCAGTGGCATTAGGCGATGGATGTGTAGGATAGGCGGGAGG CTTTGAAGCATAGGCGCCAGCTTGTGTGGAGCCCCCTGAAATACCGCCCTTCCGTCTCCTATGTCTAACCGCGATTCCGGGACCCTGCGTGGTGGGTAGT TTGACTGGGGCGGTCGCCTCCCAAAGAGTAACGGAGGCGCGCGATGGTGGGCTCAGGCCGGTCGGAAATCGGCTGATGAGTGCAATGGCAAAAGCCCGCC TGACTGCGAGAGCGACATTGAGCAGAGTCGAAAGGGTCATAGTGATCCGGTGGTCCCGGTGGAAGGGCCATCGCTCAACGGATAAAGGTACTCTGGGATA ACAGGCTGATACTGCCCAAGAGTCCACATCGACGGCAGGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGGGCTGGAGCAGGTCCAAGGGTTCGCTG TTCGCCGATAAAGTGGTACGTGAGCTGGGTTTAGAACGTGTGAGACAGTTCGGTCCCTATCTACCGTGGGTGTAGGATATTGAGAGGACTGTCCCTAGTA CGAGAGGACCGGGATGGACATACTCTGGTGTACCAGTTGTCACGCCAGTGCACGCTGGGTAGCTAAGTTGGCGGGATAACCGCTGAAACATCTAAGCGGA AGCCTCCTAAAACAGGTATCCCAGGACCGTGGAAGACCACACGTGATGGCCGG Borrelia GTAATAAGGTCTATGGTGAATGCCTAGGAGCTTAGGCGAAGAAGGTCGTGGTAACTGCGAAAAGCTTGGGGGAGAAGCAAAATTTATGATCCCAAGATTA CCGAATGTCTTTAAGACGAACCAGGGGAGTGAACCATCTAAGTACCCTGGGAAAAGAAATCAAAGAGATTCCCTTAGTAGTGGCGAGCGAAAAGGGAGTA GCCCGGATATAGAAGAATAATCTGGAAATTTAACCAAGAGGTGAAGTCCTGTATTAATCCTGAGTGGACGAGGCACGAGAAACCTTGTTTGAAGCTGGGG AGACCACTCTCCAAGGCTAAATACTAAAAGCTACCGATAGAGAAGAGTACCGTGAGGAAAGGTGAAAAGACCGGAGTGAAAAGACTGAAACCGTAGACTT ACAACAGTCAAAGCCGTCGGTGATGGGTGCCTTTTGCATAATGAACCTGCGAGTTATCATGTCTAGCAGATTAAAGACGGAGTCGAAGCGAGCGGTCTTA AAAGGGCGTAGTTAGATGTGGTAGACCCAAGCCAGTGATCTATTTATGGCCAGCTGAAGCTTGGTAAAACCAAGTGGAGGGCCGAACTAGTCTGTTTAAA AAGGCGGGATGAGTGTAATAGGAGTGAAAGGCTAAACAAACTCGAGATAGCTGGTCTCCCCGAAATGGATTTAAGTTCAGCCTTATTGTTTAATAAGGTA GAGCACTAATTGAGCTAGCCTTAGGGAAACTCAGTTAAACTCCGAATGCTATATAATAGGAGTGAGACATGGGCGATAAGGTTCATAGTCGAGAGGGAAA CAACCCAGACCAACAGCTAAGTCTCAAAAAGTGTTAAGTGGAAAGGAGGTTAGGTACGTAAACAGCCAGGAGGTTGCTTAGAAGCAGCCTTTAAAGAGTG CGTAATAGCTCACTGGTCGAGTACTTACCGATAATGTCGGCTAAACACATTACCGAAGCTTTGGATAAATGGTAGGGGAGCGTTCTGTACCAGAAAGTTA AGCTGGAAGTTTGATGGAGGTATCAGAAGTGAGAATGAGGTATGAGTAACGAAAATGGGTGAGATTCCCATTCGCCGAAAACCTAAGGTTCCTGGGTAAG GTCGTCTTCCCAGGGTTAGTCGGCCCCTAAGGCAAAGCTGAATGTAGTCGATGGGAAACGGGTAATATTCCGTACGTGACGCATAGGTTACTACTCTAGA TGGCTAGGTAGCGTGCCAAGAAATACACCGTACCAAACCGACACAGGTAGGTGGATGAAAATTCTAAGGCGGCGAGAGAATCCACGTTAAGGAACTCTGC AAAATACGTACGTAACTTCGGGATAAGTACGACCTACATAGTAGCATAAAAAGGTCCAAGACTGTTTACCAAAAACACAGGCTCTGCAAATCTGTAAAGA AAGTATAGGGACTGACACCTGCCCGGTGCTGGAAGGTTAAGAGGAGATGTTATGATTGAATTTAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCCGCACGAATGGTGTAACGATTTGGACGCTGTCTCAACGTGGAGCTCGGTGAAATTGAAGTATC GGTGAAGATCCGATTACTTGTGGTTAGACGGAAGACCCCGGAACCTTTACTATAGCTTGGTATTGAGATTTGATTAAATATGTGTAGGATAGGTGGGAGA CTTTGAAGCTATCTCGTCAGGGGTAGTGGAGTCATCTGAAATACCACCCTTGTTTAATTAGTTTCTAACTTATAAATGAGGAGAGTGCCAGGTGGGTAGT TTGACTGGGGCGGTCGCCTCCTAAAGAGTAACGGAGGTGCGCAAAGGTTACCTTAGAGTGGTTGGAAATCACTCTGTAAGTGTAAAGGCATAAGGTAGCT TAACTGTAAGACTGACAGTGAACAGATACGAAAGGGTCTTAGTGATCTGGCGGTGGCAGTGGAAGCGCCGTCACTTAACGAATAAAGGTACTCCGGGATA ACAGGCTTATCCTTCCCAAGAGTTCACATCGACGGAAGGTTTGGCACCTCGATGTCGGCTCATCGCATCCTAGGGCTGGAGCAGGTCCAAGGGTATGCTG TTCGCCATTAAAGCGGTACGCGAGCTGGGTTCAGAACGTGTGAGACAGTTTGGTCCCTATCTGCCACAAGCGTTGGATATTGAGAGGACTATCTTTAGTA CGAGAGGACCGAGATGGACGAACTCTAGTGTGCCAGTTATCCTGCCAAGGTATGCTGGGTAGCTACGTCGGAAGGATAACCGCTGAAACATCTAAGTGGA AGCCTCCTAAGAGAGATATCCTAGGGTCCTGGAAGAATACAGGTGATGGTTAG Burkholderia@mallei CGAACAAGGCATGTGGTGGATGCCTTGGCGATCAGGCGATGAAGGACGCGGTAGCTGCGAAAAGCTACGGGGAGCTGCAAAGAGCTTGATCCGTAGATGT CCGAATGTCCACATGAGCGACGCGGTGACTGAAACATCTAAGTAACCGCGGAAAAGAAATCAACGAGATTCCCAAAGTAGTGGCGAGCGAAATGGGAAGA GCCTACTGTTAGCCGAACGCTCTGGAAATGCGGCCTAGCGGTGAAGCCCTGTAGCAAAGACAAGTGGGCGGGACACGTGAAATCCTGTCTGAAGATGGGG GGACCATCCTCCAAGGCTAAATACTCTGATCGACCGATAGTGAACAGTACCGTGAGGAAAGGCGAAAAGACCGGAGTGAAAAGTCTGAAACCGCATGCAT ACAACAGTCGGAGCCTCGGGTGACGGGTACCTTTTGTATAATGGGTCAGCGACTTACGTTCAGTAGCAGCTTAACAAGGCAGGCGTAGCGAGCGGTCCGA ATAGGGCGCAGTTGCTGGGCGTAGACCCAAACCGGTGATCTATCCATGGCCAGATGAAGGTGCGTAACACGTACTGGAGGTCCGAACACTAACGTTGAAA AGTTAGGGATGAGTGTGATAGGGGTGAAAGGCTAAACAAACCTGAAATAGCTGGTCTCTCCGAAAACTATTTAGGTAGTGCCTCGTGCACCTTCGGGGTA GAGCACTGTCATGGTTGGGTCTGGATACGCCATAGCAAACTCCGAATACCGATGCACGGGAGACAGACATGGGTGCTAACGTCCGGTGTCAAGAGGGAAA CAACCCAGACCGCCAGCTAAGTCCCCAAAATGGCTAAGTGGAAACGAAGTGGAAGGCTAAAACAGTCAGGAGGTTGCTTAGAAGCAGCCTTTAAAGAAAG CGTAATAGCTCACTGATCGAGTCGTCCCGGAAGATGTCGGCTAAGCCATATACCGAAGCTGCGGATAGATGGTAGGAGAGCGTTCCGTACCTGCAAGGTG CGTTGAAAGCGTGCTGGAGGTATCGGAAGTGCGAATGTGACATGAGTAGCGAAAGGGGGTGAAAGGCCCCCTCGCCGTAAGCCCAAGGTTCCTACGCAAG TTCATCGGCGTAGGGTGAGTCGGCCCCTAAGGCGAGGCAGAACGTAGCTGATGGGAAGCAGGCAATATTCTGCACGGGACGGATGCGGAAGGTTGCCGGT TGGCCGGAATTTGTTCCAAGAAAAGCACCGTACCAAACCGACACAGGTGGGCGAGAGAGTATTCTAAGGCGTTGAGAGAACTCGGGAGAAGGAACTCGGC AAATTGGTACCGTAACTTCGGGATAAGGTACGCCCTTGAGGTTGCAATAAACGGTGGTGGACTGTTTAATAAAAACACAGCCTCTGCAAACACGAAAGTG ACGTATAGGGTGTGACGCCTGCCCGGTGCCGGAAGATTAAATGATGGGGTCAAGTCTTGATTGAAGTCCCGGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGATGGCCACACTGTCTCCTCCCGAGACTCAGCGAAGTTGAAGTGTT TGTGATGATCAATCTACCCGCGGCTAGACGGAAGACCCCAGAACCTTTACTGTAGCTTTGCATTGGACTTTGAACCGATCTGTGTAGGATAGGTGGGAGG CTATGAAACCGGAATGCTAGTTTCGGTGGAGCCTCCTGAAATACCACCCTGGTTTGTTTGGGTTCTAACCTTGATTCGGGGACAGTGCATGGTAGGCAGT TTGACTGGGGCGGTCTCCTCCCAAAGCGTAACGGAGGAGTACGAAGGTACGCTAGGTACGGTCGGAAATCGTGCTGATAGTGCAATGGCATAAGCGTGCT TAACTGCGAGACCGACAGTGAGCAGGTGCGAAAGGGTCATAGTGATCCGGTGGTTCTGATGGAAGGGCCATCGCTCAACGGATAAAGGTACTCTGGGATA ACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGGTTTGGCACCTCGATGTCGGCTCATCTCATCCTGGGGCTGTAGCCGGTCCAAGGGTATGCTG TTCGCCATTAAAGAGGTACGTGAGCTGGGTTTAAAACGTGTGAGACAGTTTGGTCCCTATCTGCCGTGGGCGTTGGAAGTTGAAGGGGCTGCTCCTAGTA CGAGAGGACCGGAGTGGACGAACTCTGGTGTACCGGTTGTGACGCCAGTCCACGCCGGGTAGCTATGTCGGAGAGATAACCGCTGAAACATCTAAGCGGG AACTCCCTAAGAGAGACTTCCCAGGGTCGTTCGAGACCAGACGTGATGGTCGG Bacillus@globisporus TTAGAAAGGCGCATGGTGGATGCCTTGGCACTAAGCCTAAGAAGGACGGCACTACACCGATATGCTCCGGGGAGCTGTAAGAAGCTTGATCCGGAGATTT CCGAATGCGTACATCGGCAACCCGGAGACTGAAACATCTAAGTATCCGGGGAATAGAAAGAAAATCGATTCCCTGAGTAGCGGCGAGCGAAACGGGAAGA GCCCGGAATTAGACGAAGGACCTGGAAAGTCCGCCTAGCGGTAAAGCCCCGTATCAAACCTGAGTCGGCGGAACACGTGAAATTCCGTCGGAATCCGGGA GGACCATCTCCCAAGGCTAAATACTCCTAGTGACCGATAGTGAACAGTACCGTGAGGAAAGGTGAAAAGCCCGGAGTGAAAAGTCTGAAACCATGTGCCT ACAATTGTCAGAGCCCAGGGTGATGGGTGCCTTTTGTAGAATGAACCGGCGAGTTACGATTCCATGCAGGTTAAGAGGGGAGCCGCAGCGAGCGGTCTGA ATAGGGCGGAGTATGGGGTCGTAGACCCAAACCGGTGATCTACCCATGTCCAGGTGAAGGTAAGTAACACTTACTGGAGGCCCGAACACGTACGTTGAAA AGTGCGGGATGAGTGTGGTAGCGGTGAAATTCCAATCGAACCTGAGATAGCTGGTCTCTCCGAAATAGCTTTAGGGCTAGCCTCAAAAGATCTCGAGGTA GAGCACTGTTTGGACTAGGCCTCGGTAAATTCAGACAAACTCCGAATGCCGATATTTGGGAGTCAGACGCGGGTGATAAGATCCGTAGTCGAGAGGGAAA CAGCCCAGACCACCAGTTAAGTCCCCAAGATCGTTAAGTGGAAAGGATGTGCGTTGCCCAGACAACCAGGATGTTGCTTAGAAGCAGCCTTTAAAGAGTG CGTAATAGCTCACTGGTCGAGTGGCGCCCGAAAATGTCGGCTAAACGAATCACCGAAACTGTGGATTAGTGGTAGGAGAGCGTTCCAAGGCGTCAAGCTA GACCGTAAGACTGGTGGAGCGCTTGGAAGTGAGAATGCGGTATGAGTAGCGAAGAAGGGTGAGAATCCCTTCCACCGAATGCCCAAGGTTCCTGAGGAAG CTCGTCCGCTCAGGGTTAGTCAGGACCTAAGTTGAGGCCGAACGTAGACGATGGACAACAGGTGATATTCTGTACGTGACGCAGAGGATAGGGTGCGCGT TGGCGCGCCCTCCTGCCAAGAAAAGCCCTGTACCAAACCGACACAGGTAGGCAGGAGAGAATCCTAAGGTGTCGAGAGAACTCTCGTTAAGGAACTCGGC AAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTCTTAGGGCCGCAGTGAATGGCCCAGGACTGTTTAGCAAAAACACAGGCTCTGCAAAACCGCAAGGT AAGTATAGGGGCTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGAGAGGTCAAGTTCGAATTGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCCGCACGAAAGGCGTAACGATCTGGGCACTGTCTCAACGAGAGACTCGGTGAAATTATAATACC TGTGAAGATCAGGTTACCCGCGACAGGACGGAAGACCCCGGGAGCTTTACTGTAACCTGATATTGAATTCCGGTGCAGCCTGTACAGGATAGGTAGGAGC CTTGGATTCCGGAGCGCTAGCTTCGGATGAGGCTTGTGGGATACTACCCTGGCTGTATTGACTTCTAACCCATATCAGGAGACAGTGTCAGGCGGGCAGT TTGACTGGGGCGGTCGCCTCCTAAAGAGTAACGGAGGCGCCCAAAGGTTCCCTCAGAATGGTCGGACATCATTCGTAGAGTGCAAAGGCATAAGGGAGCT TGACTGCGAGACCTACAGTGAGCAGGGTCGAAAGGGGCTTAGTGATCCGGTGGTTCCGATGGAAGGGCCATCGCTCAACGGATAAAGCTACCCCGGGATA ACAGGCTTATCTCCCCCAAGAGTCCACATCGACGGGGAGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGGGCTGTAGTCGGTCCAAGGGTTGGCTG TTCGCCCATAAAGCGGTACGCGAGCTGGGTTCAGAACGTGTGAGACAGTTCGGTCCCTATCCGTCGCGGGCGCAGGAAATTGAGAGGACTGTCCTTAGTA CGAGAGGACCGGGATGGACATACTCTGGTGTACCAGTTGTCTTGCCAAAGCACGCTGGGTAGCTATGTTGGCGGGATAAATGCTGAAACATCTAAGCATA AGCCCCCTGAGAGAGATTTCCCAGATCCCTCAAAGAAGATAGGTGATGGTCTG Enterococcus TGAATAAGGCGCACGGTGGATGCCTTGGCACTAAGCCGATGAAGGACGGGACTACACCGATATGCTTTGGGGAGCTGTACGAAGCTAGATCCAGAGATTT CCGAATGCGAACATCGGTAACGCAGAGACTGAAACATCTAAGTACCTGCGGAAGAGAAAGAAAATCGATTCCCTGAGTAGCGGCGAGCGAAACGGGAAAA GCCCGGAGATAGTCGAATGACTTGGAAAGTCAGTCAAGAGGTAAAACCCCGTAACAATCCTGAGTCGGCGGAACACGAGAAATTCCGTCGGAATCCGGGA GGACCATCTCCCAAGGCTAAATACTCCTAGTGACCGATAGTGAACAGTACCGTGAGGAAAGGTGAAAAGCCCGGAGTGAAAAGACTGAAACCGTGTGCCT ACAAAAGTCAAAGCCCAGGGTGATGGGTGCCTTTTGTAGAATGAACCGGCGAGTTACGATTGCATGCGGGTTAAGAAAGGAGCCGCAGCGAGCGGTCTGA ATAGGGCGGAGTATGTAGTCGTAGACCCAAACCTGTGATCTACCCATGTCCAGTTGAAGGTGCGTAAAACGCACTGGAGGACCGAACACGTACGTTGAAA AGTGCGGGATGAGTGTGGTAGCGGAGAAATTCCAAACGAACTTGAGATAGCTGGTCTCTCCGAAATAGCTTTAGGGCTAGCCTCGGAAGATGATGAGGTA GAGCACTGTTTGGACTAGGCCTTGGTAAATTCAGATAAACTCCGAATGCCATCATCCGGGAGTCAGACGTGAGTGATAAGATCCATAGTCGAAAGGGAAA CAGCCCAGACCACCAGCTAAGTCCCAAAAAATGTTAAGTGGAAAGGATGTGGGTTGCACAGACAACTAGGATGTTGCTTAGAAGCAGCCTTTAAAGAGTG CGTAATAGCTCACTAGTCGAGTGACCCCCGAAAATGTCGGCTAAACATATTACCGAAGCTGTGGAGTTTTGGTAGGAGAGCGTTCTAAGGCGTCAAGGCA GATCGTGAGACTGCTGGAGCGCTTAGAAGTGAGAATGCGGTATGAGTAGCGAAGACAGGTGAGAATCCTGTCCACCGAATGACTAAGGTTCCTGGGGAAG CTCGTCCGCCCAGGGTTAGTCGGGACCTAAGCCGAGGCCGAACGTAGGCGATGGATAACAGGTGATATTCTGTACGGGACGCAGAGGCTAAGGAACAGAT CGGTCTGTCCTCCTGCCGAGAAAAGCCCCGTACCAAACCGACACAGGTAGTCAGGAGAGAATCCTAAGGTGGCGAGAGAACTCTCGTTAAGGAACTCGGC AAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTGATAACGCCGCAGTGAATGGCCCAAGACTGTTTATCAAAAACACAGGCTCTGCAAAATCGTAAGAT AAGTATAGGGGCTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGAGTGCTCAAGTACGAATTGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCCGCACGAAAGGCGTAACGATTTGGGCACTGTCTCAACGAGAGACTCGGTGAAATTTTAGTACC TGTGAAGATCAGGTTACCCGCGACAGGACGGAAGACCCCAGGAGCTTTACTGTAGTTTGATATTGAGTGTCTGTACCGCATGTACAGGATAGGTAGGAGC CGTAGAAATCGGAACGCTAGTTTCGATGGAGGCCTGTGGGATACTACCCCTGCGTTATGGCACTCTAACCCGCATTGGGAGACAGTGTCAGATGGGCAGT TTGACTGGGGCGGTCGCCTCCTAAAAGGTAACGGAGGCGCCCAAAGGTTCCCTCAGAATGGTTGGAAATCATTCGAAGAGTGTAAAGGCAGAAGGGAGCT TGACTGCGAGACCAACAGTGAGCAGGGACGAAAGGGGCTTAGTGATCCGGTGGTTCCGATGGAAGGGCCATCGCTCAACGGATAAAGCTACCCTGGGATA ACAGGCTTATCTCCCCCAAGAGTCCACATCGACGGGGAGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGTAGTCGGTCCAAGGGTTGGCTG TTCGCCCATAAAGCGGCACGCGAGCTGGGTTCAGAACGTGTGAGACAGTTCGGTCCCTATCCGTCGCGGGCGTTGGAAATTGAGAGGACTGTCCTTAGTA CGAGAGGACCGGGATGGACTTACGCTGGTGTACCAGTTGTTCTGCCAAGGCATGCTGGGTAGCTATGTGGGAGGGATAAACGCTGAAACATCTAAGTGTA AGCCCCCTAAGAGAGATTTCCCAGATCCCTGAGAGATGATAGGTGATGGTCAG Mycobacterium@leprae TGCCTAAGGCGCATGGTGGATGCCTTGGCATCGAGCCGATGAAGGACGTGGGAGCTGCGATATGCCTCGGGGAGCTGCAACGAGCGTGATCCGAGGATTT CCGAATGCCCATATGGGGGACGCGGGGAGTGAAACATCTCAGTACCCGTGGAGAAGAAAACAATGTGATTCCGCAAGTAGTGGCGAGCGAACGTGGAATA GGCTGGAGGTAGCGGAAAGGCCTGGGATGCCTGCCTAGAGGTGAAGCCCAGTAGCAAGCCCGAGTGCAGCGGGCCCGTGGAATCTGCTGTGAATCTGCCG GGACCACCCGGTAAGCCTAAATACTTTCGATGACCGATAGCGGACAGTACCGTGAGGAATGGTGAAAAGTCCGGAGTGAAAAGACTGAAACCGTGTGCCT ACAACCGTCAGAGCCTTGGGTGATGGGTGCTTTTTGAAGAATGAGCCTGCGAGTCAGGACATGTCGCGGGTTAACTGGGTAGCCGCAGCGAGCGGTCTGA ATAGGGCGTAGTGGCGTGTTCTGGACCCAAGCGAGTGATCTACCCATGGCCAGGTGAAGCGCGGTAAGACCGCGTGGAGGCCCGAACACTTAAGTTGAAG ATTGAGGGATGAGTGTGGTAGGGGTGAAAGGCCAATCAAACTCGTGATAGCTGGTCTCCCCGAAATGCATTTAGGTGCAGCGTTGCGTTCCCACGAGGTA GAGCACTGGATGGCCGAGGCCTCGGTAACGTCAGCCAAACTCCGAATGCCGTAACGTGGCAGTGAGACGCGGGGGATAAGCTCCGTCGTCGAAAGGGAAA CAGCCCAGATCGCCGGCTAAGCCCCTAAGGGTGCTAAGTGGAAAGGATGTCAGTCGCAAAGACAACCAGGAGGTTGCTTAGAAGCAGCCTTGAAAGAGTG CGTAATAGCTCACTGGTCAAGTGATTGCCGATAATGTCGGCTAAGCACACCGCCGAAGCCGCGGCACTTGGGTAGGGGAGCGTTCCTCATCAGCAAGCCT CCGGGTAACGGTGGTGGAGGGTGGGGAAGTGAGAATGAGGCATGAGTAGCGAAGGCAAGTGAGAACCTTGCCCGCCGTAAGACCAAGGTTCCTGGGCCAG CCAGTCCGCCCAGGGTGAGTCGGGACCTAAGGCGAGGCCGAACGTAGTCGATGGACAACGGGTGATATTCCGTACGTGACGCAGAAGGTAGCCGTCCAGG TGGCTGGCGGTTCTGCCAAGAAAAGCCCCGTACCAAACCGACACAGGTGGTCGGTAGAGCATACCAAGGCGACGAGATAACTATGGTTAAGGAACTCGGC AAAATGCCTCCGTAACTTCGGGAGAAGGGGGGCCGGTTTCGTCGCAGAGACCGTGAGAGGACTGTTTACTAAAAACACAGGCCGTGCGAAGTCGTAAGAC ATGTATACGGACTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGACCTGTAAAGGGAGAATTTAAGCCCCAGTAAACGGCGGTGGTAACTATAACCATCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCTCAACTGTCTCAACCATAGACTCGGCGAAATTGCACTACG AGTAAAGATCTCGTTACGTGCGGCAGGACGAAAGACCCCGGGACCTTCACTACAACTTGGTATTGATGTTCGGTGCGGTTTGTGTAGGATAGGTGGGAGA CTGTGAAACTTCGACGCTAGTTGGGGTGGAGTCTTGTGAAATACCACTCTGATTGTATTGACATCTAACCTCGATTTAGGGACAGTGCCTGGCGGGTAGT TTAACTGGGGCGGTTGCCTCCTAAAATGTAACGGAGGCGCCCAAAGGTTCCCTCAACCTGGTCGGTAATCAGGTGGCGAGTGTAAATGCACAAGGGGGCT TGACTGCGAGACCTACAGTAAGCAGGGACGAAAGGGGATTAGTGATCCGGCACCTCTGGTGGAAGGGGTGTCGCTCAACGGATAAAGGTACCCCGGGATA ACAGGCTGATCTTCCCCAAGAGTCCATATCGACGGGATGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGAAGCAGGTCCAAGGGTTGGCTG TTCGCCCATAAAGCGGCACGCGAGCTGGGTTTAGAACGTGTGAGACAGTTCGGTCTCTATCCGCCGCGCGCGTCAGAAATTGAGGAAACTGTCCCTAGTA CGAGAGGACCGGGACGGACGAACTCTGGTATACCAGTTGTCTCACCAGGGCACGCTGGATAGCCACGTCGGCAAGATAACCGCTGAAACATCTAAGCGGA AACCTCTCAAGACAGGTTTCTTAGGCCCCCCGCAGAACACGGATGATGGTCAG Rhodococcus@erythrop TAATGAAGGCGTACGGTGGATGCCTTGGCACCAAGCCGATGAAGGACGTAGGAGCTGCGATAAGCCTCGGGGAGCTGCAACGAGCTGGATCCGAGGATGT CCGAATGCCCATATGGGGGACGTGGGGAGTGAAACATCTCAGTACCCACGGAAGAGAAAACAACGTGATTCCGTGAGTAGTGGCGAGCGAAAGCGGAAGA GGCTGGTGTTAGTGGAAGGGTCTGGAACGCCTGTCTAGAGGTGAAATCCCGTAACAAACCCAAGTGCACCGGGCCCGTGAAATCTGGTGTGAATCTGTCG GGACCACCCGATAAGCCTGAATACTCCTGGTGACCGATAGCGGATAGTACCGTGAGGAAAGGTGAAAAGTCCGGAGTGAAAAGACTGAAACCGTGCGCTT ACAACCGTCAGAGCCTTGGGTGATGGGTGCCTTTTGAAGAATGAGCCTGCGAGTTAGGGCATATCGCGGGTTAACTGGGTAGCCGTAGCGAGCGGTCCGA ATAGGGCGTAGTGGCATGCTCTAGACCCAAGCGAGTGATCTACCCATGGCCAGTTGAAGCGACGTAAGACGTCGTGGAGGACCGAACACTTAGGTTGAAA ACTGAGGGATGAGTGTGGTAGGGGTGAAAGGCCAATCAAACTCGTGATAGCTGGTCTCCCCGAAATGCATTTAGGTGCAGCGTCGCGTTCCACCGAGGTA GAGCACTGGATGGTCTAGGGCCCGCTAAAATCAGCCAAACTCCGAATGCCGGAGCGCGGCAGTGAGACGCGGGCGATAAGGTTCGTAGTCGAGAGGGAAA CAGCCCAGATCGCCAGCTAAGTCCCTAAGGGTACTAAGTGGAAAGGATGTGGGTCGCGAAGACAACCAGGAGGTTGCTTAGAAGCAGCCTTGAAAGAGTG CGTAATAGCTCACTGGTCAAGTGATCCCCGACAATGTCGGCTAAGTACACCACCGAAGCTGCGGCAACTGGGTAGGGGAGCGTCGTGTGCCATGAAGCGG CAGGGTGACTGCCGTGGAGGCCACACGAGTGAGAATGAGGCATGAGTAGCGAAGACGAGTGAGAAACTCGTCCGCCGAATGACCAAGGTTCCTGGGCCAG TTAATCCGCCCAGGGTGAGTCGGGACCTAAGACGAGGCCGAACGTAGCCGATGGACAACGGGTGATATTCCGTACGTGACGCAGAAGGTAGCTGACCAGG TGGCTGGCAGTTCTGCCGAGAAAAGCCCCGTACCAAACCGACACAGGTGGTCGGTAGAGAATACTAAGGCGTCGAGATAACTATGGTTAAGGAACTCGGC AAAATGCCCCCGTAACTTCGGGAGAAGGGGGGCCCTTTTGGCCGCAGAGACCGTGAGAGGACTGTTTACTAAAAACACAGGCCGTGCGAAGTCGTAAGAC ATGTATACGGACTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGACCGGTTCGGTGAGAATTTAAGCCCCAGTAAACGGCGGTGGTAACTATAACCATCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCTCAGCTGTCTCAACCGTAGACTCGGCGAAATTGCATTACG AGTAAAGATCTCGTTACGCGCGGCAGGACGAAAGACCCCGGGACCTTCACTACAGCTTGGTATTGGTGTTCGGTTCGGTTTGTGTAGGATAGGTGGGAGA CTGTGAAGCGGTGACGCCAGTTATCGTGGAGTCTTGTGAAATACCACTCTGATCGAATTGACCTCTAACCTCGATTCAGGGACAGTGCCTGGTGGGTAGT TTAACTGGGGCGGTTGCCTCCCAAAATGTAACGGAGGCGCCCAAAGGTTCCCTCAGCCTGGTTGGCAATCAGGTGTCGAGTGCAAGTGCACAAGGGAGCT TGACTGTGAGACTGACAGTGTGCAGGGACGAAAGGGGACTAGTGATCCGGCACCGGCAGTGGAAGCGGTGTCGCTCAACGGATAAAGGTACCCCGGGATA ACAGGCTGATCTTCCCCAAGAGTCCATATCGACGGGATGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGTAGGTCCAAGGGTTGGCTG TTCGCCCATAAAGCGGCACGCGAGCTGGGTTTAGAACGTGTGAGACAGTTCGGTCTCTATCCGCCGCGCGCGTTAGAAATTGAGGAAGCTGTCCCTAGTA CGAGAGGACCGGGACGGACGAACTCTGGTGTGCCAGTTGTTCCGCCAGGACACGCTGGTTAGCTACGTCGGAGGGATAACCGCTGAAACATCTAAGCGGA AGCCTTTCAAGAGAGGTTTCTCAGGCCCCCGGCAGACCACGGGTGATGGCCAG Mycobacterium TGTCTAAGGCGCATGGTGGATGCCTTGGCATCGAGCCGATGAAGGACGTGGGAGCTGCGATAAGCCTCGGGGAGCTGCAACGAGCGTGATCCGAGGATTT CCGAATGCCCATATGGGGGACGCGGGGAGTGAAACATCTCAGTACCCGTGGAGAAGAAAACAAAGTGATTCCGTAAGTAGTGGCGAGCGAACGCGGAACA GGCTGGAGGTAACGGAAGGGCCTGGGATGTCTGCCTAGAGGTGAAGCCCGGTAGTAAACCCGAGTGCAGCGGGCCCGTGGAATCTGCTGTGAATCTGCCG GGACCACCCGGTAAGCCTAAATACTCTCGATGACCGATAGCGGATAGTACCGTGAGGAATGGTGAAAAGTCCGGAGTGAAAAGACTGAAACCGTGTGCCT ACAACCGTCAGAGCCCCGGGTGATGGGTGCCTTTTGAAGAATGAGCCTGCGAGTCAGGACATGTCGCGGGTTAACTGGGTAGCCGCAGCGAGCGGTCTGA ATAGGGCGTAGTGGCGTGTTCTGGACCCAAGCGAGTGATCTACCCATGGCCAGGTGAAGCGCGGTAAGACCGCGTGGAGGCCCGAACACTTAGGTTGAAG ACTGAGGGATGAGTGTGGTAGGGGTGAAAGGCCAATCAAACTCGTGATAGCTGGTCTCCCCGAAATGCATTTAGGTGCAGCGTTGCGTTCCCACGAGGTA GAGCACTGGATGGCCGAGGCCCCGGTAACGTCAGCCAAACTCCGAATGCCGTATCGTGGCAGTGAGACGCGGGGGATAAGCTCCGTCGTCGAAAGGGAAA CAGCCCAGATCGCCGGCTAAGCCCCAAAGGGTGCTAAGTGGAAAGGATGTCAGTCGCAGAGACAACCAGGAGGTTGCTTAGAAGCAGCCTTGAAAGAGTG CGTAATAGCTCACTGGTCAAGTGATTGCCGATAATGTCGGCTAAGCACACCGCCGAAGCCGCGACACATGGGTAGGGGAGCGTCCCTCATCAGCAAGCTG CCGGGTGACGGTGGTGGAGGATGGGGGAGTGAGAATGAGGCATGAGTAGCGAAGGCAAGTGAGAACCTTGCCCGCCGAAAGACCAAGGTTCCTGGGCCAG CCAGTCCGCCCAGGGTGAGTCGGGACCTAAGGCGAGGCCGAACGTAGTCGATGGACAACGGGTGATATTCCGTACGTGACGCAGAAGGCAGCCGTCCAGG TGGCTGGCGGTTCTGCCAAGAAAAGCCCCGTACCAAACCGACACAGGTGGTCGGTAGAGAATACCAAGGCGACGAGATAACTATGGTTAAGGAACTCGGC AAAATGCCCCCGTAACTTCGGGAGAAGGGGGACCGGTTTCGTCGCAGAAACCGTGAGAGGACTGTTTACTAAAAACACAGGCCGTGCGAAGTCGCAAGAC ATGTATACGGACTGACGCCTGCCCGGTGCTGGAAGGTTAAGAGGACCCGTCAAGGGAGAATTTAAGCCCCAGTAAACGGCGGTGGTAACTATAACCATCC TAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCTGCACGAATGGCGTAACGACTTCTCAACTGTCTCAACCATAGACTCGGCGAAATTGCACTACG AGTAAAGATCTCGTTACGCGCGGCAGGACGAAAGACCCCGGGACCTTCACTACAACTTGGTATTGGTGTTCGGTACGGTTTGTGTAGGATAGGTGGGAGA CTGTGAAACCTCAACGCCAGTTGGGGTGGAGTCTTGTGAAATACCACTCTGATCGTATTGACACCTAACGTCGATTCACGGACAGTGCCTGGCGGGTAGT TTAACTGGGGCGGTTGCCTCCTAAAATGTAACGGAGGCGCCCAAAGGTTCCCTCAACCTGGACGGCAATCAGGTGGCGAGTGTAAGTGCACAAGGGAGCT TGACTGCGAGACCTACAGTAAGCAGGGACGAAAGGGGACTAGTGATCCGGCACCTCTGGTGGAAGGGGTGTCGCTCAACGGATAAAGGTACCCCGGGATA ACAGGCTGATCTTCCCCAAGAGTCCATATCGACGGGATGTTTGGCACCTCGATGTCGGCTCGTCGCATCCTGGGGCTGGAGCAGGTCCAAGGGTTGGCTG TTCGCCCATAAAGCGGCACGCGAGCTGGGTTTAGAACGTGTGAGACAGTTCGGTCTCTATCCGCCGCGCGCGTCAGAAGTTGAGGAAACTGTCCCTAGTA CGAGAGGACCGGGACGGACGAACTCTAGTGCACCAGTTGTCCCACCAGGGCACGCTGGATAGCTACGTCGGCAGGATAACCGCTGAAACATCTAAGCGGA AACCTCTCAAGACAGGCTTCTCAGGCCCCCCGCAGAACACGGTTGATGGCCAG bppsuite-2.4.1/Examples/Data/LSUrooted.dnd000066400000000000000000000102361333524216000203500ustar00rootroot00000000000000((Synechocystis:0.314376799802742, (((((((Streptomyces@coelico:0.013876432437002, Streptomyces@griseus:0.012745360610087):0.008666806511068, Streptomyces@rimosus:0.011399623481898):0.055437204703884, (Frankia@sp:0.035215752793328, ((Thermomonospora@chro:0.02455061178336, Thermomonospora:0.036494354399615):0.013833012299189, Microbispora:0.057839299523173):0.05726214573943):0.010627946862017):0.023152122896789, (((Mycobacterium:0.008969397259068, Mycobacterium@leprae:0.018880876651733):0.02199446036151, Mycobacterium@smegma:0.018406096469464):0.050883392606131, Rhodococcus@erythrop:0.028337950687323):0.044461942116207):0.013026675667065, (Tropheryma:0.093212049504794, Micrococcus:0.067010434625741):0.014478462001561):0.04424987656893, Renibacterium:0.065457488433629):0.125648670981682, (((Peptococcus:0.196637106255359, Clostridium@botulinu:0.168224551275553):0.026938471818237, (((Mycoplasma@hyopneumo:0.288431547362493, Ureaplasma:0.300784998600134):0.074114192596258, Erysipelothrix@rhusi:0.111818380319661):0.064639704490597, ((Enterococcus:0.027750762397806, ((Lactococcus:0.062471182452097, Streptococcus:0.043841965988075):0.046829712995486, (Lactobacillus:0.084280919180287, Leuconostoc@lactis:0.101165441542673):0.033153631700605):0.013052901284785):0.036951722277918, (Staphylococcus@pisci:0.068123462459372, ((Bacillus@stearotherm:0.070804506277138, Bacillus@licheniform:0.015310154511196):0.019279323180391, (Listeria@monocytogen:0.049375011635418, Bacillus@globisporus:0.046819517668963):0.007005604002247):0.010195875225291):0.015467910252456):0.052927080753595):0.027845498778557):0.044855929695747, (Leptospira:0.23044909424893, ((((((((Rhodospirillum:0.089931818086547, ((Rhodobacter@sphaeroi:0.034987842067928, Rhodobacter:0.035335544653576):0.015191054142223, Paracoccus:0.036864262783206):0.094142271846528):0.02464959453946, ((((Zoogloea:0.085056919690308, Agrobacterium@vitis:0.026366542902169):0.02200819906313, (Brucella:0.018051293147513, Bartonella:0.04543046180208):0.017157911574767):0.032419000513421, (Rhodopseudomonas@pal:0.008871909199023, Bradyrhizobium:0.023716479670769):0.087099173536495):0.020041227455159, Brevundimonas:0.138450047482353):0.014444067189967):0.01833643930762, Rickettsia:0.143959735405335):0.012899564376712, Zymomonas:0.150731679520719):0.087032395773863, ((((Xylella:0.111917387533229, Leucothrix:0.116537236256815):0.012388389116208, (((Aeromonas@hydrophila:0.038111296119372, (Vibrio@cholerae:0.058611936933601, (Haemophilus:0.110665120673241, (Buchnera@aphidicola:0.099243800315892, ((Klebsiella:0.009386423217678, Citrobacter:0.012139968207256):0.004533402095723, (Escherichia@coli:0.006213802650288, Salmonella@bongori:0.015043065781675):0.004968676196463):0.017984088864831):0.020500122112008):0.028882959159722):0.020315594318839):0.014767391122524, Ruminobacter:0.153288394355919):0.053282410735226, (Acinetobacter:0.087448505594648, Pseudomonas@stutzeri:0.057521645363318):0.020627644924354):0.024407271329314):0.012376540570705, (((Alcaligenes:0.042626120115521, Bordetella@bronchise:0.031445760019642):0.029600438292427, (Burkholderia@mallei:0.028973471151616, Ralstonia@solanacear:0.040491187091657):0.027821105214362):0.030552585629177, Neisseria@meningitid:0.079047344105739):0.064794054029077):0.018868983744097, Thiobacillus:0.114434887515554):0.069912133808317):0.041733778051073, (Nannocystis:0.174470527828978, Stigmatella:0.179717157455262):0.050780314331288):0.027202994295141, ((Helicobacter@pilori:0.071680812435812, Wolinella:0.043512218531665):0.0656642252617, Campylobacter@jejuni:0.118826201321209):0.173002291425032):0.032344737919401, ((Treponema:0.182944538744283, Borrelia:0.17653593769831):0.143937707986563, (Pirellula:0.33272761226311, (Simkania:0.084850728076327, (Waddlia:0.091174343545014, (Chlamydia@sp:0.034103682078636, (Chlamydia@muridarum:0.016968075983302, Chlamydophila@felis:0.035186461511793):0.0308415092333465):0.00999302095470575):0.00432560033441125):0.04719138049113225):0.01172517552343825):0.00296399773658775):0.004434578174967):0.0060990777293125):0.00465163883258125):0.0054390495067665):0.061364627392465496, ((Thermotoga:0.13557601533902, Aquifex:0.293374136025111):0.051397493061771, Thermus:0.2111229194826):0.055925577885699); bppsuite-2.4.1/Examples/Data/Myo.dnd000066400000000000000000000055711333524216000172420ustar00rootroot00000000000000(MYG_HETPO:0.39227,(MYG_MUSAN:0.0234145,(MYG_GALJA:0.0293632,MYG_GALGA:0.0455375):0.0722258):0.599322,(((MYG_CYPCA:0.167158,MYG_BRARE:0.149255):0.172378,((((MYG_THUTO:1e-06,(MYG_THUTH:1e-06,MYG_THUOB:1e-06):1e-06):1e-06,MYG_THUAL:0.015652):0.0592755,MYG_AUXRO:0.125853):0.0436622,((MYG_NOTCO:0.00798703,(MYG_GOBGI:0.00788468,(MYG_PSEGE:0.0240623,(MYG_CRYAN:0.0239015,MYG_CHIRA:0.00785369):0.0236543):1e-06):0.0078986):0.15259,MYG_TETNG:0.147714):0.0499235):0.0733475):0.699867,(((((MYG_ANAPO:1e-06,MYG_APTFO:0.198107):0.00843426,((MYG_PHAFI:0.0328705,(MYG_URILO:0.0246731,(MYG_CERMN:1e-06,MYG_AETPY:0.00791553):0.024292):0.0163525):0.00738933,MYG_CHICK:0.0326913):0.00814451):0.131801,MYG_ALLMI:0.219033):0.0133805,(MYG_VARVA:0.180729,(MYG_GRAGE:0.0195182,(MYG_CHEMY:0.0155155,MYG_CARCR:1e-06):0.044457):0.139559):0.0673932):1e-06,(((((((((MYG_HORSE:1e-06,MYG_EQUBU:1e-06):0.0939447,(MYG_PIG:0.0140951,((MYG_CEREL:1e-06,(MYG_BOVIN:0.0235415,MYG_SHEEP:0.0078088):1e-06):0.109752,((MYG_ESCGI:1e-06,(MYG_MEGNO:1e-06,(MYG_BALPH:0.00783912,MYG_BALAC:0.00773886):0.00782112):0.00785235):0.0306363,((MYG_PHYCA:1e-06,MYG_KOGSI:0.0409474):0.0541751,((MYG_ZIPCA:0.00760349,MYG_MESCA:0.00832605):0.0760967,(MYG_INIGE:0.015716,(MYG_DELLE:1e-06,(((MYG_TURTR:1e-06,MYG_DELDE:1e-06):1e-06,(MYG_ORCOR:1e-06,MYG_GLOME:0.00801161):0.00800896):0.016269,(MYG_PHOPH:1e-06,MYG_PHODA:1e-06):0.00820659):0.00837861):0.0171207):0.0185256):0.016746):1e-06):0.0621824):0.0359032):0.0116752):1e-06,((((MYG_VULCH:1e-06,(MYG_LYCPI:0.00803533,(MYG_OTOME:1e-06,MYG_CANFA:1e-06):1e-06):0.00812196):0.0817495,MYG_MELME:0.0444323):0.013239,MYG_LUTLU:0.0214521):1e-06,(((MYG_HALGR:1e-06,MYG_PHOVI:1e-06):1e-06,MYG_PHOSI:0.0243069):0.0866446,MYG_ZALCA:0.060672):0.0289244):0.0300615):0.0297566,MYG_ROUAE:0.0317498):1e-06,MYG_ERIEU:0.0493171):0.0110735,(((MYG_RABIT:0.0775593,(MYG_OCHPR:1e-06,MYG_OCHCU:0.0165651):0.0567079):0.0123179,((((MYG_SPAEH:0.0683498,MYG_CTEGU:0.0708645):1e-06,MYG_CASFI:0.0873026):1e-06,(MYG_MOUSE:0.145838,MYG_ONDZI:0.0932476):0.0136013):1e-06,(MYG_PROGU:0.02033,MYG_LAGMA:0.0231871):0.0507527):1e-06):0.0107367,((((((((MYG_PANTR:0.00817822,MYG_HUMAN:1e-06):1e-06,MYG_GORBE:0.00814592):0.00815656,MYG_PONPY:0.00806523):1e-06,(MYG_HYLSY:1e-06,MYG_HYLAG:1e-06):1e-06):0.0326819,((MYG_MACFA:0.0080833,MYG_PREEN:1e-06):1e-06,(MYG_PAPAN:1e-06,MYG_ERYPA:1e-06):1e-06):0.0106686):0.00545373,(((MYG_LAGLA:0.0250337,(MYG_SAISC:0.0249309,MYG_CEBAP:1e-06):0.00833139):0.00827946,MYG_CALJA:1e-06):1e-06,MYG_AOTTR:0.00824082):0.078286):0.0533582,(((MYG_PERPO:0.0158598,MYG_NYCCO:0.00811721):0.0248015,MYG_GALCR:0.0494704):0.0334113,MYG_LEPMU:0.0945001):0.0344433):1e-06,MYG_TUPGL:0.038834):1e-06):0.00992492):0.00178055,(MYG_ORYAF:0.0285741,(MYG_LOXAF:0.0165379,MYG_ELEMA:0.00942453):0.165762):0.0184912):0.0669892,(MYG_MACRU:0.109639,MYG_DIDMA:0.0454016):0.0191823):0.0146532,(MYG_TACAC:0.0482844,MYG_ORNAN:0.0338331):0.0805587):0.257381):0.583683):0.535044); bppsuite-2.4.1/Examples/Data/Myo.mase000066400000000000000000001173061333524216000174220ustar00rootroot00000000000000;; saved by seaview on Fri Feb 11 18:44:46 2005 ;no comment MYG_ALLMI ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------MELSDQEWKHVLDIWTKVESK--- LPEHGHEVIIRLLQEHPETQERFEK-------------------------------FKHM KTADEMKSSEKMKQHGNTVFTALGNIL---KQKGNHAEVL-------KPLAKSHALEH-K IPVKYLEFISEIIVKVIAEKYPADFGADSQAAMRKALELFRNDMASKYKEFGYQG----- ----------------- ;no comment MYG_CARCR ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDDEWNHVLGIWAKVEPD--- LSAHGQEVIIRLFQLHPETQERFAK-------------------------------FKNL TTIDALKSSEEVKKHGTTVLTALGRIL---KQKNNHEQEL-------KPLAESHATKH-K IPVKYLEFICEIIVKVIAEKHPSDFGADSQAAMKKALELFRNDMASKYKEFGFQG----- ----------------- ;no comment MYG_CHEMY ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDDEWNHVLGIWAKVEPD--- LTAHGQEVIIRLFQLHPETQERFAK-------------------------------FKNL TTIDALKSSEEVKKHGTTVLTALGRIL---KQKNNHEQEL-------KPLAESHATKH-K IPVKYLEFICEIIVKVIAEKHPSDFGADSQAAMKKALELFRNDMASKYKEFGFLG----- ----------------- ;no comment MYG_GRAGE ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDDEWHHVLGIWAKVEPD--- LSAHGQEVIIRLFQVHPETQERFAK-------------------------------FKNL KTIDELRSSEEVKKHGTTVLTALGRIL---KLKNNHEPEL-------KPLAESHATKH-K IPVKYLEFICEIIVKVIAEKHPSDFGADSQAAMRKALELFRNDMASKYKEFGFQG----- ----------------- ;no comment MYG_VARVA ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDEEWKKVVDIWGKVEPD--- LPSHGQEVIIRMFQNHPETQDRFAK-------------------------------FKNL KTLDEMKNSEDLKKHGTTVLTALGRIL---KQKGHHEAEI-------APLAQTHANTH-K IPIKYLEFICEVIVGVIAEKHSADFGADSQEAMRKALELFRNDMASRYKELGFQG----- ----------------- ;no comment MYG_AUXRO ------------------------------------------------------------ ------------------------------------------------------------ -----------------------------------------ADFDAVLKCWGPVEAD--- FNTVGGMVLARLFKDHPDTQKLFPK-------------------------------FAG- IAAGDLAGNAAVAAHGGTVLKKLGELL---KAKGNHAAII-------KPLANSHATKH-K IPINNFKLITEALVHVMQEK--AGLDAAGQTALRNVMGIVIADLEANYKELGFTG----- ----------------- ;no comment MYG_THUAL ------------------------------------------------------------ ------------------------------------------------------------ -----------------------------------------ADFDAVLKCWGPVEAD--- YTTMGGLVLTRLFKEHPETQKLFPK-------------------------------FAG- IAQADIAGNAAISAHGATVLKKLGELL---KAKGSHAAIL-------KPLANSHATKH-K IPINNFKLISEVLVKVMHEK--AGLDAGGQTALRNVMGIIIADLEANYKELGFSG----- ----------------- ;no comment MYG_THUOB ------------------------------------------------------------ ------------------------------------------------------------ -----------------------------------------ADFDAVLKCWGPVEAD--- YTTIGGLVLTRLFKEHPETQKLFPK-------------------------------FAG- IAQADIAGNAAVSAHGATVLKKLGELL---KAKGSHAAIL-------KPLANSHATKH-K IPINNFKLISEVLVKVMHEK--AGLDAGGQTALRNVMGIIIADLEANYKELGFSG----- ----------------- ;no comment MYG_THUTH ------------------------------------------------------------ ------------------------------------------------------------ -----------------------------------------ADFDAVLKCWGPVEAD--- YTTIGGLVLTRLFKEHPETQKLFPK-------------------------------FAG- IAQADIAGNAAVSAHGATVLKKLGELL---KAKGSHAAIL-------KPLANSHATKH-K IPINNFKLISEVLVKVMHEK--AGLDAGGQTALRNVMGIIIADLEANYKELGFSG----- ----------------- ;no comment MYG_THUTO ------------------------------------------------------------ ------------------------------------------------------------ -----------------------------------------ADFDAVLKCWGPVEAD--- YTTIGGLVLTRLFKEHPETQKLFPK-------------------------------FAG- IAQADIAGNAAVSAHGATVLKKLGELL---KAKGSHAAIL-------KPLANSHATKH-K IPINNFKLISEVLVKVMHEK--AGLDAGGQTALRNVMGIIIADLEANYKELGFSG----- ----------------- ;no comment MYG_CHIRA ------------------------------------------------------------ ------------------------------------------------------------ -----------------------------------------ADFDMVLKCWGPMEAD--- HATHGSLVLTRLFTEHPETLKLFPK-------------------------------FAG- IAHGDLAGDAGVSAHGATVLNKLGDLL---KARGAHAALL-------KPLSSSHATKH-K IPIINFKLIAEVIGKVMEEK--AGLDAAGQTALRNVMAIIITDMEADYKELGFTE----- ----------------- ;no comment MYG_CRYAN ------------------------------------------------------------ ------------------------------------------------------------ -----------------------------------------ADFDMVLKCWGPVEAD--- HATHGSLVLTRLFTEHPETLKLFPK-------------------------------FAG- IAHGDLAGDAGVSAHGATVLKKLGDLL---KARGGHAALL-------KPLSSSHATKH-K IPIINFTLIAEVIGKVMEEK--AGLDAAGQTALRNVMAIIITDMEADYKELGFTE----- ----------------- ;no comment MYG_GOBGI ------------------------------------------------------------ ------------------------------------------------------------ -----------------------------------------ADFDMVLKCWGPVEAD--- YTTHGSLVLTRLFTEHPETLKLFPK-------------------------------FAG- IAHGDLAGDAGVSAHGATVLNKLGDLL---KARGAHAALL-------KPLSSSHATKH-K IPIINFKLIAEVIGKVMEEK--AGLDAAGQTALRNVMAVIIADMEADYKELGFTE----- ----------------- ;no comment MYG_NOTCO ------------------------------------------------------------ ------------------------------------------------------------ -----------------------------------------ADFDMVLKCWGPMEAD--- YATHGGLVLTRLFTEHPETLKLFPK-------------------------------FAG- IAHGDLAGDAGVSAHGATVLNKLGDLL---KARGAHAALL-------KPLSSSHATKH-K IPIINFKLIAEVIGKVMEEK--AGLDAAGQTALRNVMAVIIADMEADYKELGFTE----- ----------------- ;no comment MYG_PSEGE ------------------------------------------------------------ ------------------------------------------------------------ -----------------------------------------ADFDMVLKCWGLVEAD--- YATYGSLVLTRLFTEHPETLKLFPK-------------------------------FAG- IAHGDLAGDAGVSAHGATVLNKLGDLL---KARGGHAALL-------KPLSSSHATKH-K IPIINFKLIAEVIGKVMEEK--AGLDAAGQTALRNVMAVIIADMEADYKELGFTE----- ----------------- ;no comment MYG_TETNG ------------------------------------------------------------ ------------------------------------------------------------ -----------------------------------------GDFDMVLKFWGPVEAD--- YSAHGGMVLTRLFTENPETQQLFPK-------------------------------FVG- IAQSELAGNAAVSAHGATVLKKLGELL---KAKGNHAAIL-------QPLANSHATKH-K IPIKNFKLIAEVIGKVMAEK--AGLDAAGQQALRNIMATIIADIDATYKELGFS------ ----------------- ;no comment MYG_BRARE ------------------------------------------------------------ ------------------------------------------------------------ -----------------------------------------ADHDLVLKCWGAVEAD--- YAANGGEVLNRLFKEYPDTLKLFPK-------------------------------FSG- ISQGDLAGSPAVAAHGATVLKKLGELL---KAKGDHAALL-------KPLANTHANIH-K VALNNFRLITEVLVKVMAEK--AGLDAAGQGALRRVMDAVIGDIDGYYKEIGFAG----- ----------------- ;no comment MYG_CYPCA ------------------------------------------------------------ ------------------------------------------------------------ -----------------------------------------HDAELVLKCWGGVEAD--- FEGTGGEVLTRLFKQHPETQKLFPK-------------------------------FVG- IASNELAGNAAVKAHGATVLKKLGELL---KARGDHAAIL-------KPLATTHANTH-K IALNNFRLITEVLVKVMAEK--AGLDAGGQSALRRVMDVVIGDIDTYYKEIGFAG----- ----------------- ;no comment MYG_GALGA ------------------------------------------------------------ ------------------------------------------------------------ -----------------------------------------ADWDKVNSVWSAMEAN--- ITAVGQNILLRLFEQYPESQSYFPK-------------------------------LKN- KSLGELKDTADIKAQADTVLKALGNIV---KKKGNHSQPV-------KALAATHITTH-K IPPHYFTKITTIAVGVLSEMYPSEMNAQAQEAFSGAFKSICSDIEKEYKAANFQG----- ----------------- ;no comment MYG_GALJA ------------------------------------------------------------ ------------------------------------------------------------ -----------------------------------------ABWDKVNSVWSAVEQN--- ITAIGQNILLRLFEQYPESEDYFPK-------------------------------LKN- KSLGELKDTADIKAQADTVLRALGNIV---KKKGDHSQPV-------KALAATHITTH-K IPPHYFTKITTIAVGVLSEMYPSEMNAQAQAAFSGAFKNICSDIEKEYKAANFQG----- ----------------- ;no comment MYG_MUSAN ------------------------------------------------------------ ------------------------------------------------------------ -----------------------------------------VDWEKVNSVWSAVESD--- LTAIGQNILLRLFEQYPESQNHFPK-------------------------------FKN- KSLGELKDTADIKAQADTVLSALGNIV---KKKGSHSQPV-------KALAATHITTH-K IPPHYFTKITTIAVDVLSEMYPSEMNAQVQAAFSGAFKIICSDIEKEYKAANFQG----- ----------------- ;no comment MYG_HETPO ------------------------------------------------------------ ------------------------------------------------------------ -----------------------------------------TEWEHVNKVWAVVEPD--- IPAVGLAILLRLFKEHKETKDLFPK-------------------------------FKE- IPVQQLGNNEDLRKHGVTVLRALGNIL---KQKGKHSTNV-------KELADTHINKH-K IPPKNFVLITNIAVKVLTEMYPSDMTGPMQESFSKVFTVICSDLETLYKEANFQG----- ----------------- ;no comment MYG_AETPY ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDQEWQQVLSIWGKVESD--- LAGHGHQVLMRLFQDHPETLDRFDK-------------------------------FKGL KTPDQMKGSEDLKKHGVTVLTQLGKIL---KQKGNHESEL-------KPLAQTHATKH-K IPVKYLEFISEAIMKVIAEKHAADFGGDSQAAMKKALELFRNDMASKYKEFGFQG----- ----------------- ;no comment MYG_CERMN ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDQEWQQVLSIWGKVESD--- LAGHGHQVLMRLFQDHPETLDRFEK-------------------------------FKGL KTPDQMKGSEDLKKHGVTVLTQLGKIL---KQKGNHESEL-------KPLAQTHATKH-K IPVKYLEFISEAIMKVIAEKHAADFGGDSQAAMKKALELFRNDMASKYKEFGFQG----- ----------------- ;no comment MYG_URILO ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDQEWQHVLTIWGKVESD--- LAGHGHQVLMRLFQDHPETLDRFEK-------------------------------FKGL KTPDQMKGSEDLKKHGVTVLTQLGKIL---KQKGNHESEL-------KPLAQTHATKH-K IPVKYLEFISEAIIKVIAEKHASSFGADSQAAMKKALELFRNDMASKYKEFGFQG----- ----------------- ;no comment MYG_ANAPO ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDQEWQQVLTIWGKVEAD--- LAGHGHAVLMRLFQDHPETLDRFEK-------------------------------FKGL KTPDQMKGSEDLKKHGVTVLTQLGKIL---KQKGNHEAEL-------KPLAQTHATKH-K IPVKYLEFISEVIIKVIAEKHSADFGADSQAAMKKALELFRNDMASKYKEFGFQG----- ----------------- ;no comment MYG_PHAFI ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDQEWQQVLTIWGKVESD--- LPGHGHEVLMRLFRDHPETLDRFER-------------------------------FKGL KTPDQMKASEDLKKHGVTVLTQLGKIL---KQKGNHESEL-------KPLAQTHATKH-K IPVKYLEFISEVIIKVIAEKHSADFGADSQAAMKKALELFRNDMASKYKEFGFQG----- ----------------- ;no comment MYG_CHICK ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDQEWQQVLTIWGKVEAD--- IAGHGHEVLMRLFHDHPETLDRFDK-------------------------------FKGL KTPDQMKGSEDLKKHGATVLTQLGKIL---KQKGNHESEL-------KPLAQTHATKH-K IPVKYLEFISEVIIKVIAEKHAADFGADSQAAMKKALELFRNDMASKYKEFGFQG----- ----------------- ;no comment MYG_APTFO ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLNDQEWQQVLTMWGKVESD--- LAGHGHAVLMRLFKSHPETMDRFDK-------------------------------FRGL KTPDEMRGSEDMKKHGVTVLT-LGQIL---KKKGHHEAEL-------KPLSQTHATKH-K VPVKYLEFISEAIMKVIAQKHASNFGADAQEAMKKALELFRNDMASKYKEFGFQG----- ----------------- ;no comment MYG_ORNAN ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLKVWGKVEGD--- LPGHGQEVLIRLFKTHPETLEKFDK-------------------------------FKGL KTEDEMKASADLKKHGGTVLTALGNIL---KKKGQHEAEL-------KPLAQSHATKH-K ISIKFLEYISEAIIHVLQSKHSADFGADAQAAMGKALELFRNDMAAKYKEFGFQG----- ----------------- ;no comment MYG_TACAC ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLKVWGKVETD--- ITGHGQDVLIRLFKTHPETLEKFDK-------------------------------FKHL KTEDEMKASADLKKHGGVVLTALGSIL---KKKGQHEAEL-------KPLAQSHATKH-K ISIKFLEFISEAIIHVLQSKHSADFGADAQAAMGKALELFRNDMATKYKEFGFQG----- ----------------- ;no comment MYG_DIDMA ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNAWGKVEAD--- IPGHGQEVLIRLFKGHPETLEKFDK-------------------------------FKHL KSEDEMKASEDLKKHGATVLTALGNIL---KKKGNHEAEL-------KPLAQSHATKH-K ISVQFLEFISEAIIQVIQSKHPGDFGGDAQAAMGKALELFRNDMAAKYKELGFQG----- ----------------- ;no comment MYG_MACRU ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNIWGKVETD--- EGGHGKDVLIRLFKGHPETLEKFDK-------------------------------FKHL KSEDEMKASEDLKKHGITVLTALGNIL---KKKGHHEAEL-------KPLAQSHATKH-K IPVQFLEFISDAIIQVIQSKHAGNFGADAQAAMKKALELFRHDMAAKYKEFGFQG----- ----------------- ;no comment MYG_AOTTR ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNVWGKVEAD--- VPSHGQEVLISLFKGHPETLEKFDK-------------------------------FKHL KSEDEMKASEELKKHGVTVLTALGGIL---KKKGHHEAEL-------KPLAQSHATKH-K IPVKYLEFISDAIVHVLQKKHPGDFGADAQGAMKKALELFRNDMAAKYKELGFQG----- ----------------- ;no comment MYG_CALJA ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNVWGKVEAD--- IPSHGQEVLISLFKGHPETLEKFDK-------------------------------FKHL KSEDEMKASEELKKHGVTVLTALGGIL---KKKGHHEAEL-------KPLAQSHATKH-K IPVKYLEFISDAIVHVLQKKHPGDFGADAQGAMKKALELFRNDMAAKYKELGFQG----- ----------------- ;no comment MYG_CEBAP ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNVWGKVEAD--- IPSHGQEVLISLFKGHPETLEKFDK-------------------------------FKHL KSEDEMKASEELKKHGATVLTALGGIL---KKKGQHEAEL-------KPLAQSHATKH-K IPVKYLEFISDAIVHVLQKKHPGDFGADAQGAMKKALELFRNDMAAKYKELGFQG----- ----------------- ;no comment MYG_SAISC ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNIWGKVEAD--- IPSHGQEVLISLFKGHPETLEKFDK-------------------------------FKHL KSEDEMKASEELKKHGTTVLTALGGIL---KKKGQHEAEL-------KPLAQSHATKH-K IPVKYLELISDAIVHVLQKKHPGDFGADAQGAMKKALELFRNDMAAKYKELGFQG----- ----------------- ;no comment MYG_LAGLA ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNIWGKVEAD--- IPSHGQEVLISLFKGHPETLEKFDK-------------------------------FKHL KSEDEMKASEELKKHGVTVLTALGGIL---KKKGQHEAEL-------KPLAQSHATKH-K IPVKYLEFISDAIIHALQKKHPGDFGADAQGAMKKALELFRNDMAAKYKELGFQG----- ----------------- ;no comment MYG_ERYPA ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNVWGKVEAD--- IPSHGQEVLIRLFKGHPETLEKFDK-------------------------------FKHL KSEDEMKASEDLKKHGATVLTALGGIL---KKKGHHEAEI-------KPLAQSHATKH-K IPVKYLELISESIIQVLQSKHPGDFGADAQGAMNKALELFRNDMAAKYKELGFQG----- ----------------- ;no comment MYG_PAPAN ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNVWGKVEAD--- IPSHGQEVLIRLFKGHPETLEKFDK-------------------------------FKHL KSEDEMKASEDLKKHGATVLTALGGIL---KKKGHHEAEI-------KPLAQSHATKH-K IPVKYLELISESIIQVLQSKHPGDFGADAQGAMNKALELFRNDMAAKYKELGFQG----- ----------------- ;no comment MYG_PREEN ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNVWGKVEAD--- IPSHGQEVLIRLFKGHPETLEKFDK-------------------------------FKHL KSEDEMKASEDLKKHGATVLTALGGIL---KKKGHHEAEI-------KPLAQSHATKH-K IPVKYLELISESIIQVLQSKHPGDFGADAQGAMNKALELFRNDMAAKYKELGFQG----- ----------------- ;no comment MYG_MACFA ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNVWGKVEAD--- IPSHGQEVLIRLFKGHPETLEKFDK-------------------------------FKHL KSEDEMKASEDLKKHGVTVLTALGGIL---KKKGHHEAEI-------KPLAQSHATKH-K IPVKYLELISESIIQVLQSKHPGDFGADAQGAMNKALELFRNDMAAKYKELGFQG----- ----------------- ;no comment MYG_GORBE ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNVWGKVEAD--- ISGHGQEVLIRLFKGHPETLEKFDK-------------------------------FKHL KSEDEMKASEDLKKHGATVLTALGGIL---KKKGHHEAEI-------KPLAQSHATKH-K IPVKYLEFISECIIQVLQSKHPGDFGADAQGAMNKALELFRKDMASNYKELGFQG----- ----------------- ;no comment MYG_HUMAN ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNVWGKVEAD--- IPGHGQEVLIRLFKGHPETLEKFDK-------------------------------FKHL KSEDEMKASEDLKKHGATVLTALGGIL---KKKGHHEAEI-------KPLAQSHATKH-K IPVKYLEFISECIIQVLQSKHPGDFGADAQGAMNKALELFRKDMASNYKELGFQG----- ----------------- ;no comment MYG_PANTR ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNVWGKVEAD--- IPGHGQEVLIRLFKGHPETLEKFDK-------------------------------FKHL KSEDEMKASEDLKKHGATVLTALGGIL---KKKGHHEAEI-------KPLAQSHATKH-K IPVKYLEFISECIIQVLHSKHPGDFGADAQGAMNKALELFRKDMASNYKELGFQG----- ----------------- ;no comment MYG_HYLAG ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNVWGKVEAD--- IPSHGQEVLIRLFKGHPETLEKFDK-------------------------------FKHL KSEDEMKASEDLKKHGATVLTALGGIL---KKKGHHEAEI-------KPLAQSHATKH-K IPVKYLEFISECIIQVLQSKHPGDFGADAQGAMNKALELFRKDMASNYKELGFQG----- ----------------- ;no comment MYG_HYLSY ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNVWGKVEAD--- IPSHGQEVLIRLFKGHPETLEKFDK-------------------------------FKHL KSEDEMKASEDLKKHGATVLTALGGIL---KKKGHHEAEI-------KPLAQSHATKH-K IPVKYLEFISECIIQVLQSKHPGDFGADAQGAMNKALELFRKDMASNYKELGFQG----- ----------------- ;no comment MYG_PONPY ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNVWGKVEAD--- IPSHGQEVLIRLFKGHPETLEKFDK-------------------------------FKHL KSEDEMKASEDLKKHGATVLTALGGIL---KKKGHHEAEI-------KPLAQSHATKH-K IPVKYLEFISESIIQVLQSKHPGDFGADAQGAMNKALELFRKDMASNYKELGFQG----- ----------------- ;no comment MYG_CTEGU ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNAWGKVETD--- IGGHGQEVLIRLFKGHPETLEKFDK-------------------------------FKHL KSEDEMKASEDLKKHGTTVLTALGNIL---KKKGQHEAEL-------APLAQSHATKH-K IPVKYLEFISEAIIQVLESKHPGDFGADAQGAMSKALELFRNDIAAKYKELGFQG----- ----------------- ;no comment MYG_ERIEU ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNVWGKVEAD--- IPGHGQEVLIRLFKDHPETLEKFDK-------------------------------FKHL KSEDEMKSSEDLKKHGTTVLTALGGIL---KKKGQHEAQL-------APLAQSHANKH-K IPVKYLEFISEAIIQVLKSKHAGDFGADAQGAMSKALELFRNDIAAKYKELGFQG----- ----------------- ;no comment MYG_ROUAE ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNVWGKVEAD--- IPGHGQEVLIRLFKGHPETLEKFDK-------------------------------FKHL KSEDEMKASEDLKKHGATVLTALGGIL---KKKGQHEAQL-------KPLAQSHATKH-K IPVKYLEFISEVIIQVLQSKHPGDFGADAQGAMGKALELFRNDIAAKYKELGFQG----- ----------------- ;no comment MYG_LAGMA ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNVWGKVEAD--- LGGHGQEVLIRLFKGHPETLEKFDK-------------------------------FKHL KAEDEMRASEDLKKHGTTVLTALGGIL---KKRGQHAAEL-------APLAQSHATKH-K IPVKYLEFISEAIIQVLQSKHPGDFGADAQAAMSKALELFRNDIAAKYKELGFQG----- ----------------- ;no comment MYG_PROGU ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNVWGKVEGD--- LSGHGQEVLIRLFKGHPETLEKFDK-------------------------------FKHL KAEDEMRASEELKKHGTTVLTALGGIL---KKKGQHAAEL-------APLAQSHATKH-K IPVKYLEFISEAIIQVLQSKHPGDFGADAQGAMSKALELFRNDIAAKYKELGFQG----- ----------------- ;no comment MYG_ORYAF ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDAEWQLVLNVWGKVEAD--- IPGHGQDVLIRLFKGHPETLEKFDR-------------------------------FKHL KTEDEMKASEDLKKHGTTVLTALGGIL---KKKGQHEAEI-------QPLAQSHATKH-K IPVKYLEFISEAIIQVIQSKHSGDFGADAQGAMSKALELFRNDIAAKYKELGFQG----- ----------------- ;no comment MYG_MELME ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNVWGKVEAD--- LAGHGQEVLIRLFKGHPETLEKFDK-------------------------------FKHL KSEDEMKGSEDLKKHGNTVLTALGGIL---KKKGHQEAEL-------KPLAQSHATKH-K IPVKYLEFISDAIAQVLQSKHPGNFAAEAQGAMKKALELFRNDIAAKYKELGFQG----- ----------------- ;no comment MYG_LUTLU ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNVWGKVEAD--- LAGHGQEVLIRLFKGHPETLEKFDK-------------------------------FKHL KSEDEMKGSEDLKKHGNTVLTALGGIL---KKKGKHEAEL-------KPLAQSHATKH-K IPIKYLEFISEAIIQVLQSKHPGBFGADAQGAMKRALELFRNDIAAKYKELGFQG----- ----------------- ;no comment MYG_CASFI ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLHVWGKVEAD--- LAGHGQEVLIRLFKGHPETLEKFNK-------------------------------FKHI KSEDEMKASEDLKKHGVTVLTALGGVL---KKKGHHEAEI-------KPLAQSHATKH-K IPIKYLEFISEAIIHVLQSKHPGBFGADABGAMNKALELFRKDIAAKYKELGFQG----- ----------------- ;no comment MYG_ONDZI ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLHVWGKVEAD--- LAGHGQDVLIRLFKAHPETLEKFDK-------------------------------FKHI KSEDEMKGSEDLKKHGBTVLTALGGIL---KKKGHHEAEI-------KPLAQSHATKH-K IPIKYLEFISEAIIHVLZSKHPSBFGADVZGAMKRALELFRNDIAAKYKELGFQG----- ----------------- ;no comment MYG_CANFA ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQIVLNIWGKVETD--- LAGHGQEVLIRLFKNHPETLDKFDK-------------------------------FKHL KTEDEMKGSEDLKKHGNTVLTALGGIL---KKKGHHEAEL-------KPLAQSHATKH-K IPVKYLEFISDAIIQVLQSKHSGDFHADTEAAMKKALELFRNDIAAKYKELGFQG----- ----------------- ;no comment MYG_OTOME ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQIVLNIWGKVETD--- LAGHGQEVLIRLFKNHPETLDKFDK-------------------------------FKHL KTEDEMKGSEDLKKHGNTVLTALGGIL---KKKGHHEAEL-------KPLAQSHATKH-K IPVKYLEFISDAIIQVLQSKHSGDFHADTEAAMKKALELFRNDIAAKYKELGFQG----- ----------------- ;no comment MYG_LYCPI ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQIVLNIWGKVETD--- LAGHGQEVLIRLFKNHPETLDKFDK-------------------------------FKHL KTEDEMKGSEDLKKHGNTVLTALGGIL---KKKGHHEAEL-------KPLAQSHATKH-K IPVKYLEFISDAIIQVLQNKHSGDFHADTEAAMKKALELFRNDIAAKYKELGFQG----- ----------------- ;no comment MYG_VULCH ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNIWGKVETD--- LAGHGQEVLIRLFKNHPETLDKFDK-------------------------------FKHL KTEDEMKGSEDLKKHGNTVLTALGGIL---KKKGHHEAEL-------KPLAQSHATKH-K IPVKYLEFISDAIIQVLQSKHSGDFHADTEAAMKKALELFRNDIAAKYKELGFQG----- ----------------- ;no comment MYG_ZALCA ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNIWGKVEAD--- LVGHGQEVLIRLFKGHPETLEKFDK-------------------------------FKHL KSEDEMKRSEDLKKHGKTVLTALGGIL---KKKGHHDAEL-------KPLAQSHATKH-K IPIKYLEFISEAIIHVLQSKHPGDFGADTHAAMKKALELFRNDIAAKYRELGFQG----- ----------------- ;no comment MYG_BALAC ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------VLSDAEWHLVLNIWAKVEAD--- VAGHGQDILIRLFKGHPETLEKFDK-------------------------------FKHL KTEAEMKASEDLKKHGNTVLTALGGIL---KKKGHHEAEL-------KPLAQSHATKH-K IPIKYLEFISDAIIHVLHSRHPAEFGADAQAAMNKALELFRKDIAAKYKELGFQG----- ----------------- ;no comment MYG_BALPH ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------VLTDAEWHLVLNIWAKVEAD--- VAGHGQDILISLFKGHPETLEKFDK-------------------------------FKHL KTEAEMKASEDLKKHGNTVLTALGGIL---KKKGHHEAEL-------KPLAQSHATKH-K IPIKYLEFISDAIIHVLHSRHPADFGADAQAAMNKALELFRKDIAAKYKELGFQG----- ----------------- ;no comment MYG_MEGNO ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------VLSDAEWQLVLNIWAKVEAD--- VAGHGQDILIRLFKGHPETLEKFDK-------------------------------FKHL KTEAEMKASEDLKKHGNTVLTALGGIL---KKKGHHEAEL-------KPLAQSHATKH-K IPIKYLEFISDAIIHVLHSRHPADFGADAQAAMNKALELFRKDIAAKYKELGFQG----- ----------------- ;no comment MYG_ESCGI ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------VLSDAEWQLVLNIWAKVEAD--- VAGHGQDILIRLFKGHPETLEKFDK-------------------------------FKHL KTEAEMKASEDLKKHGNTVLTALGGIL---KKKGHHEAEL-------KPLAQSHATKH-K IPIKYLEFISDAIIHVLHSRHPGDFGADAQAAMNKALELFRKDIAAKYKELGFQG----- ----------------- ;no comment MYG_KOGSI ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------VLSEGEWQLVLHVWAKVEAD--- IAGHGQDILIRLFKHHPETLEKFDR-------------------------------FKHL KSEAEMKASEDLKKHGVTVLTALGAIL---KKKGHHEAEL-------KPLAQSHATKH-K IPIKYLEFISEAIIHVLHSRHPADFGADAQGAMSKALELFRKDIAAKYKELGYQG----- ----------------- ;no comment MYG_PHYCA ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------VLSEGEWQLVLHVWAKVEAD--- VAGHGQDILIRLFKSHPETLEKFDR-------------------------------FKHL KTEAEMKASEDLKKHGVTVLTALGAIL---KKKGHHEAEL-------KPLAQSHATKH-K IPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFRKDIAAKYKELGYQG----- ----------------- ;no comment MYG_MESCA ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSEAEWQLVLHVWAKVEAD--- LSGHGQEILIRLFKGHPETLEKFDK-------------------------------FKHL KSEAEMKASEDLKKHGHTVLTALGGIL---KKKGHHEAEL-------KPLAQSHATKH-K IPIKYLEFISDAIIHVLHSKHPSDFGADAQGAMTKALELFRKDIAAKYKELGFHG----- ----------------- ;no comment MYG_ZIPCA ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSEAEWQLVLHVWAKVEAD--- LSGHGQEILIRLFKGHPETLEKFDK-------------------------------FKHL KSEAEMKASEDLKKHGHTVLTALGGIL---KKKGHHEAEL-------KPLAQSHATKH-K IPIKYLEFISDAIIHVLHSRHPSDFGADAQAAMTKALELFRKDIAAKYKELGFHG----- ----------------- ;no comment MYG_DELDE ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNVWGKVEAD--- LAGHGQDVLIRLFKGHPETLEKFDK-------------------------------FKHL KTEADMKASEDLKKHGNTVLTALGAIL---KKKGHHDAEL-------KPLAQSHATKH-K IPIKYLEFISEAIIHVLHSRHPAEFGADAQGAMNKALELFRKDIAAKYKELGFHG----- ----------------- ;no comment MYG_TURTR ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNVWGKVEAD--- LAGHGQDVLIRLFKGHPETLEKFDK-------------------------------FKHL KTEADMKASEDLKKHGNTVLTALGAIL---KKKGHHDAEL-------KPLAQSHATKH-K IPIKYLEFISEAIIHVLHSRHPAEFGADAQGAMNKALELFRKDIAAKYKELGFHG----- ----------------- ;no comment MYG_ORCOR ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNVWGKVEAD--- LAGHGQDILIRLFKGHPETLEKFDK-------------------------------FKHL KTEADMKASEDLKKHGNTVLTALGAIL---KKKGHHDAEL-------KPLAQSHATKH-K IPIKYLEFISEAIIHVLHSRHPAEFGADAQGAMNKALELFRKDIAAKYKELGFHG----- ----------------- ;no comment MYG_GLOME ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNVWGKVEAD--- LAGHGQDILIRLFKGHPETLEKFDK-------------------------------FKHL KTEADMKASEDLKKHGNTVLTALGAIL---KKKGHHEAEL-------KPLAQSHATKH-K IPIKYLEFISEAIIHVLHSRHPAEFGADAQGAMNKALELFRKDIAAKYKELGFHG----- ----------------- ;no comment MYG_PHODA ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSEGEWQLVLNVWGKVEAD--- LAGHGQDVLIRLFKGHPETLEKFDK-------------------------------FKHL KTEAEMKASEDLKKHGNTVLTALGGIL---KKKGHHDAEL-------KPLAQSHATKH-K IPIKYLEFISEAIIHVLHSRHPAEFGADAQGAMNKALELFRKDIATKYKELGFHG----- ----------------- ;no comment MYG_PHOPH ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSEGEWQLVLNVWGKVEAD--- LAGHGQDVLIRLFKGHPETLEKFDK-------------------------------FKHL KTEAEMKASEDLKKHGNTVLTALGGIL---KKKGHHDAEL-------KPLAQSHATKH-K IPIKYLEFISEAIIHVLHSRHPAEFGADAQGAMNKALELFRKDIATKYKELGFHG----- ----------------- ;no comment MYG_DELLE ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSEGEWQLVLXXXXKVEAD--- LAGHGQDVLIRLFKGHPETLEKFDK-------------------------------FKHL KTXXXMKASEDLKKHGNTVLTALGGIL---KKKGHHEAEL-------KPLAQSHATKH-K IPIKYLXXXXEAIIHVLHSRHPAEFGADAQGAMNKALELFRKDIAAKYKELGFHG----- ----------------- ;no comment MYG_INIGE ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNIWGKVEAD--- LAGHGQDVLIRLFKGHPETLEKFDK-------------------------------FKHL KTEAEMKASEDLKKHGNTVLTALGGIL---KKKGHHEAEL-------KPLAQSHATKH-K IPIKYLEFISEAIIHVLHSRHPGDFGADAQAAMNKALELFRKDIAAKYKELGFHG----- ----------------- ;no comment MYG_HALGR ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWHLVLNVWGKVETD--- LAGHGQEVLIRLFKSHPETLEKFDK-------------------------------FKHL KSEDDMRRSEDLRKHGNTVLTALGGIL---KKKGHHEAEL-------KPLAQSHATKH-K IPIKYLEFISEAIIHVLHSKHPAEFGADAQAAMKKALELFRNDIAAKYKELGFHG----- ----------------- ;no comment MYG_PHOVI ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWHLVLNVWGKVETD--- LAGHGQEVLIRLFKSHPETLEKFDK-------------------------------FKHL KSEDDMRRSEDLRKHGNTVLTALGGIL---KKKGHHEAEL-------KPLAQSHATKH-K IPIKYLEFISEAIIHVLHSKHPAEFGADAQAAMKKALELFRNDIAAKYKELGFHG----- ----------------- ;no comment MYG_PHOSI ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWHLVLNVWGKWETD--- LAGHGQEVLIRLFKSHPETLEKFDK-------------------------------FKHL KSEDDMRRSFDLRKHGNTVLTALGGIL---KKKGHHEAEL-------KPLAQSHATKH-K IPIKYLEFISEAIIHVLHSKHPAEFGADAQAAMKKALELFRNDIAAKIKELGFHG----- ----------------- ;no comment MYG_BOVIN ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNAWGKVEAD--- VAGHGQEVLIRLFTGHPETLEKFDK-------------------------------FKHL KTEAEMKASEDLKKHGNTVLTALGGIL---KKKGHHEAEV-------KHLAESHANKH-K IPVKYLEFISDAIIHVLHAKHPSDFGADAQAAMSKALELFRNDMAAQYKVLGFHG----- ----------------- ;no comment MYG_CEREL ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNAWGKVEAD--- VAGHGQEVLIRLFTGHPETLEKFDK-------------------------------FKHL KTEAEMKASEDLKKHGNTVLTALGGIL---KKKGHHEAEV-------KHLAESHANKH-K IPVKYLEFISDAIIHVLHAKHPSNFGADAQGAMSKALELFRNDMAAQYKVLGFQG----- ----------------- ;no comment MYG_SHEEP ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNAWGKVEAD--- VAGHGQEVLIRLFTGHPETLEKFDK-------------------------------FKHL KTEAEMKASEDLKKHGNTVLTALGGIL---KKKGHHEAEV-------KHLAESHANKH-K IPVKYLEFISDAIIHVLHAKHPSNFGADAQGAMSKALELFRNDMAAEYKVLGFQG----- ----------------- ;no comment MYG_EQUBU ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQQVLNVWGKVEAD--- IAGHGQEVLIRLFTGHPETLEKFDK-------------------------------FKHL KTEAEMKASEDLKKHGTVVLTALGGIL---KKKGHHEAEL-------KPLAQSHATKH-K IPIKYLEFISDAIIHVLHSKHPGDFGADAQGAMTKALELFRNDIAAKYKELGFQG----- ----------------- ;no comment MYG_HORSE ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQQVLNVWGKVEAD--- IAGHGQEVLIRLFTGHPETLEKFDK-------------------------------FKHL KTEAEMKASEDLKKHGTVVLTALGGIL---KKKGHHEAEL-------KPLAQSHATKH-K IPIKYLEFISDAIIHVLHSKHPGDFGADAQGAMTKALELFRNDIAAKYKELGFQG----- ----------------- ;no comment MYG_ELEMA ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWELVLKTWGKVEAD--- IPGHGETVFVRLFTGHPETLEKFDK-------------------------------FKHL KTEGEMKASEDLKKQGVTVLTALGGIL---KKKGHHEAEI-------QPLAQSHATKH-K IPIKYLEFISDAIIHVLQSKHPAEFGADAQGAMKKALELFRNDIAAKYKELGFQG----- ----------------- ;no comment MYG_LOXAF ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWELVLKTWGKVEAD--- IPGHGEFVLVRLFTGHPETLEKFDK-------------------------------FKHL KTEGEMKASEDLKKQGVTVLTALGGIL---KKKGHHEAEI-------QPLAQSHATKH-K IPIKYLEFISDAIIHVLQSKHPAEFGADAQAAMKKALELFRNDIAAKYKELGFQG----- ----------------- ;no comment MYG_LEPMU ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNVWGKVEAD--- VGGHGQEVLIRLFTGHPETLEKFDK-------------------------------FKHL KTADEMKASEDLKKHGTTVLTALGGIL---KKKGQHEAEL-------KPLAQSHATKH-K IPIKYLEFISDAIVHVLHSKHPAEFGADAQAAMKKALELFRNDIAAKYKELGFQG----- ----------------- ;no comment MYG_RABIT ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDAEWQLVLNVWGKVEAD--- LAGHGQEVLIRLFHTHPETLEKFDK-------------------------------FKHL KSEDEMKASEDLKKHGNTVLTALGAIL---KKKGHHEAEI-------KPLAQSHATKH-K IPVKYLEFISEAIIHVLHSKHPGDFGADAQAAMSKALELFRNDIAAQYKELGFQG----- ----------------- ;no comment MYG_GALCR ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLKIWGKVEAD--- LAGHGQDVLIRLFTAHPETLEKFDK-------------------------------FKNL KTADEMKASEDLKKHGVTVLTALGGIL---KKKGQHEAEI-------KPLAQSHATKH-K IPVKYLEFISEAIIHVLQNKHSGDFGTDVQGAMSKALELFRNDIAAKYKELGFQG----- ----------------- ;no comment MYG_NYCCO ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQSVLNVWGKVEAD--- LAGHGQEILIRLFTAHPETLEKFDK-------------------------------FKNL KTPDEMKASEDLKKHGVTVLTALGGIL---KKKGQHEAEI-------KPLAQSHATKH-K IPVKYLEFISGAIIHVLQSKHPGDFGADAQGAMSKALELFRNDIAAKYKELGFQG----- ----------------- ;no comment MYG_PERPO ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQSVLNVWGKVEAD--- LAGHGQEILIRLFTAHPETLEKFDK-------------------------------FKNL KTPDEMKASEDLKKHGVTVLTALGGIL---KKKGHHEAEI-------KPLAQSHATKH-K IPVKYLEFISEAIIHVLQSKHPGDFGADAQGAMNKALELFRNDIAAKYKELGFQG----- ----------------- ;no comment MYG_MOUSE ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNVWGKVEAD--- LAGHGQEVLIGLFKTHPETLDKFDK-------------------------------FKNL KSEEDMKGSEDLKKHGCTVLTALGTIL---KKKGQHAAEI-------QPLAQSHATKH-K IPVKYLEFISEIIIEVLKKRHSGDFGADAQGAMSKALELFRNDIAAKYKELGFQG----- ----------------- ;no comment MYG_SPAEH ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNVWGKVEGD--- LAGHGQEVLIKLFKNHPETLEKFDK-------------------------------FKHL KSEDEMKGSEDLKKHGNTVLTALGGIL---KKKGQHAAEI-------QPLAQSHATKH-K IPIKYLEFISEAIIQVLQSKHPGDFGADAQGAMSKALELFRNDIAAKYKELGFQG----- ----------------- ;no comment MYG_OCHCU ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLTVWGKVEAD--- LAGHGQEVLIRLFKNHPETLEKFDK-------------------------------FKNL KSEDEMKGSDDLKKHGNTVLSALGGIL---KKKGQHEAEL-------KPLAQSHATKH-K IPVKYLEFISEAIIQVLQSKHPGDFGADAQGAMSKALELFRNDMAAKYKELGFHG----- ----------------- ;no comment MYG_OCHPR ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNVWGKVEAD--- LAGHGQEVLIRLFKNHPETLEKFDK-------------------------------FKNL KSEDEMKGSDDLKKHGNTVLSALGGIL---KKKGQHEAEL-------KPLAQSHATKH-K IPVKYLEFISEAIIQVLQSKHPGDFGADAQGAMSKALELFRNDMAAKYKELGFQG----- ----------------- ;no comment MYG_PIG ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNVWGKVEAD--- VAGHGQEVLIRLFKGHPETLEKFDK-------------------------------FKHL KSEDEMKASEDLKKHGNTVLTALGGIL---KKKGHHEAEL-------TPLAQSHATKH-K IPVKYLEFISEAIIQVLQSKHPGDFGADAQGAMSKALELFRNDMAAKYKELGFQG----- ----------------- ;no comment MYG_TUPGL ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------------GLSDGEWQLVLNVWGKVEAD--- VAGHGQEVLIRLFKGHPETLEKFDK-------------------------------FKHL KTEDEMKASEDLKKHGNTVLSALGGIL---KKKGQHEAEI-------KPLAQSHATKH-K IPVKYLEFISEAIIQVLQSKHPGDFGADAQAAMSKALELFRNDIAAKYKELGFQG----- ----------------- bppsuite-2.4.1/Examples/Data/OutGroup.txt000066400000000000000000000000471333524216000203250ustar00rootroot00000000000000Monodelphi Echinops, Loxodonta, Dasypusbppsuite-2.4.1/Examples/Data/lysozymeLarge.dnd000077500000000000000000000012111333524216000213320ustar00rootroot00000000000000(((((6.langur_Sen&Sve:0.007845, 7.langur_Tob&Tfr:0.000000, 8.Douc_langur_Pne:0.023560):0.008106, 9.probiscis_Nla:0.007578):0.026768, 5.colobus_Cgu&Can:0.037526):0.075806, (((10.baboon_Pcy:0.007941, 11.mangabey_Cat:0.000000):0.000000, 12.rhesus_Mmu:0.007917):0.000000, 13.Allen_Ani:0.015927, (14.talapoin_Mta:0.015990, (15.patas_Epa:0.016008, 16.vervet_Cae:0.007968):0.007936):0.008006):0.021414):0.041539, (((1.human:0.015901, 2.chimp_bonobo_gorilla:0.000000):0.007955, 3.orangutan_Ppy:0.000000):0.007230, 4.gibbon_Ggo:0.032960):0.068614, (17.squirrel_m:0.026657, (18.tamarin_Soe:0.032259, 19.Marmoset_Cja:0.040606):0.000000):0.128818); bppsuite-2.4.1/Examples/Data/lysozymeLarge.fasta000066400000000000000000000216241333524216000216720ustar00rootroot00000000000000 >1.human AAGGTCTTTG AAAGGTGTGA GTTGGCCAGA ACTCTGAAAA GATTGGGAAT GGATGGCTAC AGGGGAATCA GCCTAGCAAA CTGGATGTGT TTGGCCAAAT GGGAGAGTGG TTACAACACA CGAGCTACAA ACTACAATGC TGGAGACAGA AGCACTGATT ATGGGATATT TCAGATCAAT AGCCGCTACT GGTGTAATGA TGGCAAAACC CCAGGAGCAG TTAATGCCTG TCATTTATCC TGCAGTGCTT TGCTGCAAGA TAACATCGCT GATGCTGTAG CTTGTGCAAA GAGGGTTGTC CGTGATCCAC AAGGCATTAG AGCATGGGTG GCATGGAGAA ATCGTTGTCA AAACAGAGAT GTCCGTCAGT ATGTTCAAGG TTGTGGAGTG >2.chimp_bonobo_gorilla AAGGTCTTTG AAAGGTGTGA GTTGGCCAGA ACTCTGAAAA GATTGGGAAT GGATGGCTAC AGGGGAATCA GCCTAGCAAA CTGGATGTGT TTGGCCAAAT GGGAGAGTGG TTATAACACA CGAGCTACAA ACTACAATGC TGGAGACAGA AGCACTGATT ATGGGATATT TCAGATCAAT AGCCGCTACT GGTGTAATGA TGGCAAAACC CCAGGAGCAG TTAATGCCTG TCATTTATCC TGCAGTGCTT TGCTGCAAGA TAACATCGCT GATGCTGTAG CTTGTGCAAA GAGGGTTGTC CGTGATCCAC AAGGCATTAG AGCATGGGTG GCATGGAGAA ATCGTTGTCA AAACAGAGAT GTCCGTCAGT ATGTTCAAGG TTGTGGAGTA >3.orangutan_Ppy AAGGTCTTTG AAAGGTGTGA GTTGGCCAGA ACTCTGAAAA GATTGGGAAT GGATGGCTAC AGGGGAATCA GCCTAGCAAA CTGGATGTGT TTGGCCAAAT GGGAGAGTGG TTATAACACA CGAGCTACAA ACTACAATCC TGGAGACAGA AGCACTGATT ATGGGATATT TCAGATCAAT AGCCGCTACT GGTGTAATGA TGGCAAAACC CCAGGAGCAG TTAATGCCTG TCATTTATCC TGCAGTGCTT TGCTGCAAGA TAACATCGCT GATGCTGTAG CTTGTGCAAA GAGGGTTGTC CGTGATCCAC AAGGCATTAG AGCATGGGTG GCATGGAGAA ATCGTTGTCA AAACAGAGAT GTCCGTCAGT ATGTTCAAGG TTGTGGAGTA >4.gibbon_Ggo AAGGTCTTTG AAAGGTGTGA GTTGGCCAGA ACTCTGAAAA GATTGGGAAT GGATGGCTAC AGGGGAATCA GCCTAGCAAA CTGGATGTGT TTGGCCAAAT GGGAGAGTGG TTATAACACA CGAGCTACAA ACTACAATCC TGGAGACAGA AGCACTGATT ATGGGATATT TCAGATCAAT AGCCGCTACT GGTGTAATGA TGGCAAAACC CCAGGAGCAG TTAATGCCTG TCATTTATCC TGCAATGCTT TGCTGCAAGA TAACATCGCC GATGCTGTAG CTTGTGCAAA GAGGGTTGTC CGCGATCCAC AAGGCATTAG AGCATGGGTG GCATGGAGAA ATCGTTGTCA AAACAGAGAT CTCCGTCAGT ATATTCAAGG TTGTGGAGTA >5.colobus_Cgu&Can AAGATCTTTG AAAGGTGTGA GTTGGCCAGA ACTCTGAAAA AATTGGGACT GGATGGCTAC AAGGGAGTCA GCCTAGCAAA CTGGGTGTGT TTGGCCAAAT GGGAGAGTGG TTATAACACA GACGCTACAA ACTACAATCC TGGAGATGAA AGCACTGATT ATGGGATATT TCAGATCAAT AGCCGCTACT GGTGTAATAA TGGCAAAACC CCAGGAGCAG TTAATGCCTG TCATATATCC TGCAATGCTT TGCTGCAAAA TAACATCGCT GATGCTGTAG CTTGTGCAAA GAGGGTTGTC AGTGATCCAC AAGGCATTCG AGCATGGGTG GCATGGAAAA AGCACTGTCA AAACAGAGAT GTCAGTCAGT ATGTTGAAGG TTGTGGAGTA >6.langur_Sen&Sve AAGATCTTTG AAAGGTGTGA GTTGGCCAGA ACTCTGAAAA AATTGGGACT GGATGGCTAC AAGGGAGTCA GCCTAGCAAA CTGGGTGTGT TTGGCCAAAT GGGAGAGTGG TTATAACACA GAAGCTACAA ACTACAATCC TGGAGACGAA AGCACTGATT ATGGCATATT TCAGATCAAT AGCCGCTACT GGTGTAATAA TGGCAAAACC CCAGGAGCAG TTGATGCCTG TCATATATCC TGCAGTGCTT TGCTGCAAAA TAACATCGCT GATGCTGTAG CTTGTGCAAA GAGGGTTGTC AGTGATCCAC AAGGCATTCG AGCATGGGTG GCATGGAGAA ATCACTGTCA AAACAAAGAT GTCAGTCAGT ACGTTAAAGG TTGTGGAGTA >7.langur_Tob&Tfr AAGATCTTTG AAAGGTGTGA GTTGGCCAGA ACTCTGAAAA AATTGGGACT GGATGGCTAC AAGGGAGTCA GCCTAGCAAA CTGGGTGTGT TTGGCCAAAT GGGAGAGTGG TTATAACACA GAAGCTACAA ACTACAATCC TGGAGACGAA AGCACTGATT ATGGGATATT TCAGATCAAT AGCCGCTACT GGTGTAATAA TGGCAAAACC CCAGGAGCAG TTGATGCCTG TCATATATCC TGCAGTGCTT TGCTGCAAAA TAACATCGCT GATGCTGTAG CTTGTGCAAA GAGGGTTGTC AGTGATCCAC AAGGCATTCG AGCATGGGTG GCATGGAGAA ATCACTGTCA AAACAAAGAT GTCAGTCAGT ACGTTAAAGG TTGTGGAGTA >8.Douc_langur_Pne AAGATCTTTG AAAGGTGTGA GTTGGCCAGA ACTCTGAAAA AATTGGGACT GGATGGCTAC AAGGGAGTCA GCCTAGCAAA CTGGGTGTGT TTGGCCAAAT GGGAGAGTGG TTATAACACA GAAGCTACAA ACTACAATCC TGGAGACGAA AGCACTGATT ATGGGATATT TCAGATCAAT AGCCGCTACT GGTGTAATAA TGGCAAAACC CCAGGAGCAG TTGATGCCTG TCATATATCC TGCAGTGCTT TGCTGCAAAA CAACATCGCT GATGCTGTAG CTTGTGCAAA GAGGGTTGTC AGTGATCCAC AAGGCGTTCG AGCATGGGTG GCATGGAGAA ATCACTGTCA AAACAAAGAT GTCAGTCAGT ACGTTAAAGG TTGTGGAGTG >9.probiscis_Nla AAGATCTTTG AAAGGTGTGA GTTGGCCAGA ACTCTGAAAA AATTGGGACT GGATGGCTAC AAGGGAGTCA GCCTAGCAAA CTGGGTGTGT TTGGCCAAAT GGGAGAGTGG TTATAACACA GAAGCTACAA ACTACAATCC TGGAGACGAA AGCACTGATT ATGGGATATT TCAGATCAAT AGCCGCTACT GGTGTAATAA TGGCAAAACC CCAGGAGCAG TTGATGCCTG TCATATATCC TGCAGTGCTT TGCTGCAAAA TAACATCGCT GATGCTGTAG CTTGTGCAAA GAGGGTTGTC AGTGATCCAC AAGGCATTCG AGCATGGGTG GCATGGAGAA ATCACTGTCA AAACAGAGAT GTCAGTCAGT ACGTTAAAGG TTGTGGAGTG >10.baboon_Pcy AAGATCTTTG AAAGGTGTGA GTTGGCCAGA ACTCTGAAAA GATTGGGACT GGATGGCTAC AGGGGAATCA GCCTAGCAAA CTGGGTGTGT TTGGCCAAAT GGGAGAGTGA TTATAACACA CAAGCTACAA ACTACAATCC TGGAGACCAA AGCACTGATT ATGGGATATT TCAGATCAAT AGCCACTACT GGTGTAATAA TGGCAAAACC CCAGGAGCAG TTAATGCCTG TCATATATCC TGCAATGCTT TGCTGCAAGA TAACATCGCT GATGCTGTAA CTTGTGCAAA GAGGGTGGTC AGTGATCCAC AAGGCATTAG AGCATGGGTG GCATGGAGAA ATCACTGTCA AAACAGAGAT GTCAGTCAGT ATGTTCAAGG TTGTGGAGTG >11.mangabey_Cat AAGATCTTTG AAAGGTGTGA GTTGGCCAGA ACTCTGAAAA GATTGGGACT GGATGGCTAC AGGGGAATCA GCCTAGCAAA CTGGGTGTGT TTGGCCAAAT GGGAGAGTGA TTATAACACA CAAGCTACAA ACTACAATCC TGGAGACCAA AGCACTGATT ATGGGATATT TCAGATCAAT AGCCACTACT GGTGTAATAA TGGCAAAACC CCAGGAGCAG TTAATGCCTG TCATATATCC TGCAATGCTT TGCTGCAAGA TAACATCGCT GATGCTGTAA CTTGTGCAAA GAGGGTTGTC AGTGATCCAC AAGGCATTAG AGCATGGGTG GCATGGAGAA ATCACTGTCA AAACAGAGAT GTCAGTCAGT ATGTTCAAGG TTGTGGAGTG >12.rhesus_Mmu AAGATCTTTG AAAGGTGTGA GTTGGCCAGA ACTCTGAAAA GATTGGGACT GGATGGCTAC AGGGGAATCA GCCTAGCAAA CTGGGTGTGT TTGGCCAAAT GGGAGAGTAA TTATAACACA CAAGCTACAA ACTACAATCC TGGAGACCAA AGCACTGATT ATGGGATATT TCAGATCAAT AGCCACTACT GGTGTAATAA TGGCAAAACC CCAGGAGCAG TTAATGCCTG TCATATATCC TGCAATGCTT TGCTGCAAGA TAACATCGCT GATGCTGTAA CTTGTGCAAA GAGGGTTGTC AGTGATCCAC AAGGCATTAG AGCATGGGTG GCATGGAGAA ATCACTGTCA AAACAGAGAT GTCAGTCAGT ATGTTCAAGG TTGTGGAGTG >13.Allen_Ani AAGATCTTTG AAAGGTGTGA GTTGGCCAGA ACTCTGAAAA GATTGGGACT GGATGGCTAC AGGGGAATCA GCCTAGCAAA CTGGGTGTGT TTGGCCAAAT GGGAGAGTGA TTATAACACA CAAGCTACAA ACTACAATCC TGGAGACCAA AGCACTGATT ATGGGATATT TCAGATCAAT AGCCACTACT GGTGTAATAA TGGCAAAACC CCAGGAGCAG TTAATGCCTG TCGTATATCC TGCAATGCTT TGCTGCAAGA TAACATCGCT GATGCTGTAA CTTGTGCAAA GAGGGTTGTC AGAGATCCAC AAGGCATTAG AGCATGGGTG GCATGGAGAA ATCACTGTCA AAACAGAGAT GTCAGTCAGT ATGTTCAAGG TTGTGGAGTG >14.talapoin_Mta AAGATCTTTG AAAGGTGTGA GTTGGCCAGA ACTCTGAAAA GATTGGGACT GGATGGCTAC AGGGGAATTA GCCTAGCAAA CTGGGTGTGT TTGGCCAAAT GGGAGAGTGA TTATAACACA CAAGCTACAA ACTACAATCC TGGAGACCAA AGCACTGATT ATGGGATATT TCAGATCAAT AGCCACTACT GGTGTAATAA TGGCAAAACC CCAGGAGCAG TTAATGCCTG TCATATATCC TGCAATGCTT TGCTGCAAGA TAACATCGCT GATGCTGTAA CTTGTGCAAA GAGGGTTGTC CGTGATCCAC AAGGCATTAG AGCATGGGTG GCATGGAGAA ATCACTGTCA CAACAGAGAT GTCAGTCAGT ATGTTCAAGG TTGTGGAGTG >15.patas_Epa AAGATCTTTG AAAGGTGTGA GTTGGCCAGA ACTCTGAAAA GATTGGGACT GGATGGCTAC AGGGGAATCA GCCTAGCAAA CTGGGTGTGT TTGGCCAAAT GGGAGAGTGG TTATAACACA CAAGCTACAA ACTACAATCC TGGAGACCAA AGCACTGATT ATGGGATATT TCAGATCAAT AGCCACTACT GGTGTAATAA TGGCAAAACC CCAGGAGCAG TTAATGCCTG TCATATATCC TGCAATGCTT TGCTGCAGGA TAACATTGCT GATGCTGTAA CTTGTGCAAA GAGGGTTGTC CGTGATCCAC AAGGCATTAG AGCATGGGTG GCATGGAGAA ATCACTGTCA AAACAGAGAT GTCAGTCAGT ATGTTCAAGG TTGTGGAGTG >16.vervet_Cae AAGATCTTTG AAAGGTGTGA GTTGGCCAGA ACTCTGAAAA GATTGGGACT GGATGGCTAC AGGGGAATCA GCCTAGCAAA CTGGGTGTGC TTGGCCAAAT GGGAGAGTGG TTATAACACA CAAGCTACAA ACTACAATCC TGGAGACCAA AGCACTGATT ATGGGATATT TCAGATCAAT AGCCACTACT GGTGTAATAA TGGCAAAACC CCAGGAGCAG TTAATGCCTG TCATATATCC TGCAATGCTT TGCTGCAAGA TAACATCGCT GATGCTGTAA CTTGTGCAAA GAGGGTTGTC CGTGATCCAC AAGGCATTAG AGCATGGGTG GCATGGAGAA ATCACTGTCA AAACAGAGAT GTCAGTCAGT ATGTTCAAGG TTGTGGAGTG >17.squirrel_m AAGGTCTTCG AAAGGTGTGA GTTGGCCAGA ACTCTGAAAA GGCTTGGAAT GGATGGCTAC AGGGGAATCA GCCTAGCAAA CTGGATGTGT TTGGCCAAAT GGGAGAGTGA CTATAACACA CGTGCTACAA ACTACAATCC TGGAGACCAA AGCACTGATT ATGGGATATT TCAGATCAAT AGCCACTATT GGTGTAATAA TGGCAGAACC CCAGGAGCAG TTAATGCCTG TCATATATCC TGCAATGCTT TGCTGCAAGA TGACATCACT CAAGCTGTGG CCTGTGCAAA GAGGGTTGTC CGTGATCCAC AAGGCATTAG AGCATGGGTG GCATGGAAAG CTCATTGTCA AAACAGAGAT GTCAGTCAGT ATGTTCAAGG TTGTGGAGTA >18.tamarin_Soe AAGGTCTTCG AAAGGTGTGA GTTGGCCAGA ACTCTGAAAA GACTTGGATT GGATGGCTAC AGGGGAATCA GCCTAGCAAA CTGGATGTGT TTGGCCAAAT GGGAGAGTGA TTATAACACA CGTGCTACAA ACTACAATCC TGGAGACCAA AGCACTGATT ATGGGATATT TCAGATCAAT AGCCACTATT GGTGTAATAA CGGCAGAACC CCAGGAGCAG TTAATGCCTG TCATATATCC TGCAATGCTT TGCTGCAAGA TGACATCACT GAAGCTGTGG CCTGTGCAAA GAGGGTTGTC CGTGATCCAC AAGGCATTAG AGCATGGGTG GCATGGAAAG CTCATTGTCA AAACAGAGAT GTCAGTCAGT ATATTCAAGG TTGTGGAGTA >19.Marmoset_Cja AAGGTCTTTG AAAGGTGTGA GTTGGCCAGA ACTCTGAAAA GGTTTGGACT GGATGGCTAC AGGGGAATCA GCCTAGCAAA CTGGATGTGT TTGGCCAAAT GGGAGAGTGA TTATAACACA CGTGCTACAA ACTACAATCC TGGAGACCAA AGCACTGATT ATGGGATATT TCAGATCAAT AGCCACTATT GGTGTAACAA TGGCAGAACC CCAGGAGCAG TTAATGCCTG TCATATATCC TGCAATGCTT TGCTGCAAGA TGACATCACT GAAGCTGTGG CCTGTGCAAA GAGGGTTGTC CGCGATCCAC AAGGCATTAG GGCATGGGTG GCATGGAAAG CTCATTGTCA AAACAGAGAT GTCAGTCAGT ATGTTCAAGG TTGTGGAGTA bppsuite-2.4.1/Examples/Data/treeList.dnd000066400000000000000000003657501333524216000203010ustar00rootroot00000000000000(((((((((SHREWxxxxx:0.219983,MOLExxxxxx:0.167702):0.010260,HEDGEHOGxx:0.347021):0.020333,(((PHYLLOSTOM:0.201959,FLYINGFOXx:0.125752):0.035554,(((TAPIRxxxxx:0.079326,RHINOxxxxx:0.075323):0.012151,HORSExxxxx:0.085678):0.040927,((DOGxxxxxxx:0.136314,CATxxxxxxx:0.101515):0.040180,PANGOLINxx:0.208542):0.008352):0.005551):0.005257,(LLAMAxxxxx:0.146282,((COWxxxxxxx:0.135217,(HIPPOxxxxx:0.098291,(WHALExxxxx:0.049927,DELPHINOID:0.073922):0.047888):0.016116):0.015684,PIGxxxxxxx:0.134387):0.010244):0.034295):0.007656):0.023475,(TREESHREWx:0.211351,(((RABBITxxxx:0.127367,PIKAxxxxxx:0.182866):0.071183,((SCIURIDxxx:0.172109,CAVIOMORPH:0.287153):0.012904,(RATxxxxxxx:0.098200,MOUSExxxxx:0.098253):0.205257):0.018911):0.010892,((STREPSIRRH:0.170548,HUMANxxxxx:0.184608):0.017791,FLYINGLEMU:0.173936):0.010490):0.003670):0.014141):0.013854,((SLOTHxxxxx:0.124711,ANTEATERxx:0.149464):0.023779,ARMADILLOx:0.138961):0.048931):0.010653,(((SHEARELESH:0.132238,LOEARELESH:0.113354):0.132007,(AARDVARKxx:0.166065,(TENRECIDxx:0.284372,GOLDENMOLE:0.147378):0.018191):0.003889):0.010691,((SIRENIANxx:0.120496,ELEPHANTxx:0.161741):0.008471,HYRAXxxxxx:0.184031):0.028197):0.036082):0.207210,PLATYPUSxx:0.400376):0.211233,DIPROTODON:0.123168):0.083813,MONODELPHI:0.103535,DIDELPHISx:0.106478); 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bppsuite-2.4.1/Examples/Data/treeList2.dnd000066400000000000000000000036471333524216000203550ustar00rootroot00000000000000(Bos:0.205584,((Canis:0.058216,((Homo:0.001967,Pan:0.001103):0.008098,Macaca:0.009522):0.039742):0.004001,Monodelphi:0.211427):0.024030,Mus:0.092989); (Bos:0.120233,Canis:0.094952,(Echinops:0.173577,(((Homo:0.003880,Pan:0.002546):0.013839,Macaca:0.017396):0.061331,Mus:0.219930):0.014190):0.013808); (Bos:0.076722,Canis:0.060130,((((Homo:0.002672,Pan:0.004034):0.011988,Macaca:0.016051):0.048883,Rattus:0.161269):0.008651,Monodelphi:0.387129):0.013304); (Bos:0.140669,Canis:0.097859,((((Homo:0.001371,Pan:0.005121):0.015410,Macaca:0.020432):0.063729,Mus:0.299535):0.010901,Monodelphi:0.517359):0.026373); (Bos:0.095763,Canis:0.060316,((Echinops:0.111147,Monodelphi:0.307070):0.018958,((((Homo:0.000704,Pan:0.002084):0.009436,Macaca:0.011362):0.027452,(Mus:0.016834,Rattus:0.020162):0.076952):0.004317,Oryctolagu:0.086691):0.009698):0.013782); (Bos:0.063857,Canis:0.035719,(Echinops:0.080994,(((Homo:0.002011,Pan:0.001339):0.010075,Macaca:0.010344):0.063345,((Mus:0.030672,Rattus:0.037650):0.083515,Oryctolagu:0.053611):0.061425):0.003301):0.009376); (Bos:0.076748,Canis:0.056575,((((Homo:0.002809,Pan:0.002310):0.010931,Macaca:0.014765):0.050236,(Mus:0.064262,Rattus:0.055484):0.196583):0.009419,Monodelphi:0.403673):0.009926); (Bos:0.078125,Canis:0.064070,(Dasypus:0.079868,((Homo:0.003842,Pan:0.004556):0.009951,Macaca:0.012049):0.047785):0.026879); (Bos:0.091493,Canis:0.050625,(((Dasypus:0.062693,Monodelphi:0.267243):0.011416,((Homo:0.002103,Pan:0.001874):0.008115,Macaca:0.012615):0.044339):0.008765,(Mus:0.045525,Rattus:0.080160):0.159360):0.013926); (Bos:0.049938,Canis:0.054797,(((Dasypus:0.070434,Loxodonta:0.052947):0.000283,Monodelphi:0.454108):0.008862,(((Homo:0.002669,Pan:0.001356):0.004995,Macaca:0.009575):0.027205,Oryctolagu:0.066500):0.006027):0.008433); (Bos:0.164955,(Canis:0.083869,(((Homo:0.005534,Pan:0.004047):0.013564,Macaca:0.035816):0.068362,Oryctolagu:0.080227):0.008167):0.018262,(Monodelphi:0.355625,Rattus:0.209124):0.020357); bppsuite-2.4.1/Examples/Distance/000077500000000000000000000000001333524216000166605ustar00rootroot00000000000000bppsuite-2.4.1/Examples/Distance/Dist.bpp000066400000000000000000000035441333524216000202740ustar00rootroot00000000000000# Global variables: DATA = LSU METHOD = bionj # Sequences: # The alphabet to use: # DNA, RNA or Protein alphabet=DNA # The sequence file to use (sequences must be aligned!) input.sequence.file=../Data/$(DATA).phy # The alignment format: input.sequence.format=Phylip(order=sequential, type=extended) #Sites to use: # all, nogap or complete (=only resolved chars) input.sequence.sites_to_use = complete # Specify a maximum amount of gaps: may be an absolute number or a percentage. input.sequence.max_gap_allowed=100% # Output the distance matrix if any. output.matrix.file = $(DATA).mat # ---------------------------------------------------------------------------------------- # Model specification # ---------------------------------------------------------------------------------------- # See the manual for a description of the syntax and available options. # model = HKY85(kappa=2.843, theta=0.5, theta1=0.5, theta2=0.5, useObservedFrequencies=yes) rate_distribution = Gamma(n=4, alpha=0.358) # Tree reconstruction method [wpgma|upgma|nj|bionj] method = $(METHOD) // Parameter estimation: // - init = keep as initial values, // - pairwise = estimate separately for each pair of sequences, // - iterations = use iterations and ML to estimate these parameters globally. optimization.method = init optimization.verbose = 1 optimization.ignore_parameter = optimization.max_number_f_eval = 10000 optimization.tolerance = 0.000001 optimization.message_handler = $(DATA).messages optimization.profiler = $(DATA).profile # Should we write the resulting tree? none or file name. output.tree.file = $(DATA).$(METHOD).dnd output.tree.format = Newick # Bootstrap: bootstrap.number = 10 bootstrap.approximate = no # Set this to yes for detailed output when bootstrapping. bootstrap.verbose = no bootstrap.output.file = $(DATA).$(METHOD)_bstrees.dnd bppsuite-2.4.1/Examples/Drawing/000077500000000000000000000000001333524216000165215ustar00rootroot00000000000000bppsuite-2.4.1/Examples/Drawing/TreeDraw.bpp000066400000000000000000000005011333524216000207350ustar00rootroot00000000000000input.tree.file=../Data/LSU.dnd input.tree.format=Newick output.drawing.file=LSU.svg output.drawing.format=Svg() output.drawing.plot=Phylogram(xu=300, yu=12, direction.h=left2right, direction.v=bottom2top, draw.leaves=yes) //output.drawing.plot=Phylogram(xu=300, yu=12, direction.h=left2right, direction.v=top2bottom) bppsuite-2.4.1/Examples/MaximumLikelihood/000077500000000000000000000000001333524216000205475ustar00rootroot00000000000000bppsuite-2.4.1/Examples/MaximumLikelihood/Codons/000077500000000000000000000000001333524216000217745ustar00rootroot00000000000000bppsuite-2.4.1/Examples/MaximumLikelihood/Codons/BranchModel/000077500000000000000000000000001333524216000241525ustar00rootroot00000000000000bppsuite-2.4.1/Examples/MaximumLikelihood/Codons/BranchModel/ML.bpp000066400000000000000000000136551333524216000251770ustar00rootroot00000000000000#Example data set adapted from PAML # #logL = 65442.80353609310986939818 # Global variables: DATA = lysozymeLarge # Sequences: # The alphabet to use: # DNA, RNA or Protein... alphabet=Codon(letter=DNA) genetic_code=Standard # The sequence file to use (sequences must be aligned!) input.sequence.file=../../../Data/$(DATA).fasta # The alignment format: input.sequence.format=Fasta #Sites to use: # all, nogap or complete (=only resolved chars) input.sequence.sites_to_use = all # Specify a maximum amount of gaps: may be an absolute number or a percentage. input.sequence.max_gap_allowed = 50% input.sequence.max_unresolved_allowed = 100% input.sequence.remove_stop_codons = yes # ---------------------------------------------------------------------------------------- # Input tree file # ---------------------------------------------------------------------------------------- # user or random init.tree = user input.tree.file = ../../../Data/$(DATA).dnd input.tree.format = Newick init.brlen.method = Input # ---------------------------------------------------------------------------------------- # Model specification # ---------------------------------------------------------------------------------------- # See the manual for a description of the syntax and available options. # model = YN98(kappa=1, omega=1, frequencies=F1X4) nonhomogeneous=one_per_branch #These lines are for the F1X4 option: #nonhomogeneous_one_per_branch.shared_parameters=YN98.kappa,\ # YN98.freq_Codon.123_Full.theta, YN98.freq_Codon.123_Full.theta1, YN98.freq_Codon.123_Full.theta2 #These lines are for the F3X4 option: nonhomogeneous_one_per_branch.shared_parameters=YN98.kappa, YN98.123_* nonhomogeneous.stationarity=yes #Only if stationarity is set to false: nonhomogeneous.root_freq= rate_distribution = Constant() //Gamma(n=4, alpha=0.358) # Likelihood recursion option: # - simple: derivatives takes more time to compute, but likelihood computation is faster. # For big data sets, it can save a lot of memory usage too, particularly when the data are compressed. # - double: Uses more memory and need more time to compute likelihood, due to the double recursion. # Analytical derivatives are however faster to compute. # This option has no effect in the following cases: # - Topology estimation: this requires a double recursive algorithm, # - Optimization with a molecular clock: a simple recursion with data compression is used in this case, # due to the impossibility of computing analytical derivatives. likelihood.recursion = simple # Site compression for the simple recursion: # - simple: identical sites are not computed twice # - recursive: look for site patterns to save computation time during optimization, but # requires extra time for building the patterns. # This is usually the best option, particularly for nucleotide data sets. likelihood.recursion_simple.compression = recursive # ---------------------------------------------------------------------------------------- # Optimization # ---------------------------------------------------------------------------------------- # Should we reestimate likelihood parameters? Tree topology will not be optimized. # (recommanded) optimization = FullD(derivatives=Newton) # Tell if the parameter should be transformed in order to remove constraints. # This can improves the optimization, but might be a bit slower. optimization.reparametrization = no # Final optimization step, may be useful if numerical derivatives are used: # powell or simplex or none. optimization.final = none # Set the quantity of output to the screen: optimization.verbose = 3 # Parameters to ignore (for instance equilibrium frequencies) optimization.ignore_parameters = # Maximum number of likelihood evaluations: optimization.max_number_f_eval = 10000 # Precision to reach: optimization.tolerance = 0.000001 # idem for error or warning messages: optimization.message_handler = $(DATA).messages # A file where to dump optimization steps (a file path or std for standard output) optimization.profiler = $(DATA).profile # Shall we optimize tree topology as well? optimization.topology = no # Algorithm to use for topology estimation: only NNI for now optimization.topology.algorithm = NNI # NNI method: fast, better or phyml # You should use the phyml option, since it is really more efficient! optimization.topology.algorithm_nni.method = phyml # Number of phyml topology movement steps before reoptimizing parameters: optimization.topology.nstep = 4 # Shall we estimate parameters before looking for topology movements? optimization.topology.numfirst = no # Tolerances: These numbers should not be too low, in order to save computation # time and also for a better topology estimation. # The optimization.tolerance parameter will be used for the final optimization # of numerical parameters. # # Tolerance for the prior-topology estimation optimization.topology.tolerance.before = 100 # Tolerance for the during-topology estimation optimization.topology.tolerance.during = 100 # Shall we first scale the tree before optimizing parameters? [deprecated] optimization.scale_first = no # Should we write the resulting tree? none or file name. output.tree.file = $(DATA).ML.dnd output.tree.format = Newick # Alignment information log file (site specific rates, etc): output.infos = $(DATA).infos # Write numerical parameter estimated values: output.estimates = $(DATA).params.txt # ---------------------------------------------------------------------------------------- # Bootstrap # ---------------------------------------------------------------------------------------- bootstrap.number = 0 # Tell if numerical parameters should be kept to their initial value when bootstrapping: bootstrap.approximate = no # Set this to yes for detailed output when bootstrapping. bootstrap.verbose = no bootstrap.output.file = $(DATA).ML_bstrees.dnd bppsuite-2.4.1/Examples/MaximumLikelihood/Codons/CladeModel/000077500000000000000000000000001333524216000237655ustar00rootroot00000000000000bppsuite-2.4.1/Examples/MaximumLikelihood/Codons/CladeModel/ML.bpp000066400000000000000000000140711333524216000250030ustar00rootroot00000000000000#Example data set adapted from PAML # #logL = 65442.80353609310986939818 # Global variables: DATA = lysozymeLarge # Sequences: # The alphabet to use: # DNA, RNA or Protein... alphabet=Codon(letter=DNA) genetic_code=Standard # The sequence file to use (sequences must be aligned!) input.sequence.file=../../../Data/$(DATA).fasta # The alignment format: input.sequence.format=Fasta #Sites to use: # all, nogap or complete (=only resolved chars) input.sequence.sites_to_use = all # Specify a maximum amount of gaps: may be an absolute number or a percentage. input.sequence.max_gap_allowed = 50% input.sequence.max_unresolved_allowed = 100% input.sequence.remove_stop_codons = yes # ---------------------------------------------------------------------------------------- # Input tree file # ---------------------------------------------------------------------------------------- # user or random init.tree = user input.tree.file = ../../../Data/$(DATA).dnd input.tree.format = Newick init.brlen.method = Input # ---------------------------------------------------------------------------------------- # Model specification # ---------------------------------------------------------------------------------------- # See the manual for a description of the syntax and available options. # nonhomogeneous=general nonhomogeneous.number_of_models=2 model1 = YN98(kappa=1, omega=1, frequencies=F1X4) model1.nodes_id = 0:20 model2 = YN98(kappa=YN98.kappa_1, omega=1, frequencies=F1X4) model2.nodes_id = 21:32 #These lines are for the F1X4 option: #nonhomogeneous_one_per_branch.shared_parameters=YN98.kappa,\ # YN98.freq_Codon.123_Full.theta, YN98.freq_Codon.123_Full.theta1, YN98.freq_Codon.123_Full.theta2 #These lines are for the F3X4 option: #nonhomogeneous_one_per_branch.shared_parameters=YN98.kappa, YN98.123_* nonhomogeneous.stationarity=yes #Only if stationarity is set to false: nonhomogeneous.root_freq= rate_distribution = Constant() //Gamma(n=4, alpha=0.358) # Likelihood recursion option: # - simple: derivatives takes more time to compute, but likelihood computation is faster. # For big data sets, it can save a lot of memory usage too, particularly when the data are compressed. # - double: Uses more memory and need more time to compute likelihood, due to the double recursion. # Analytical derivatives are however faster to compute. # This option has no effect in the following cases: # - Topology estimation: this requires a double recursive algorithm, # - Optimization with a molecular clock: a simple recursion with data compression is used in this case, # due to the impossibility of computing analytical derivatives. likelihood.recursion = simple # Site compression for the simple recursion: # - simple: identical sites are not computed twice # - recursive: look for site patterns to save computation time during optimization, but # requires extra time for building the patterns. # This is usually the best option, particularly for nucleotide data sets. likelihood.recursion_simple.compression = recursive # ---------------------------------------------------------------------------------------- # Optimization # ---------------------------------------------------------------------------------------- # Should we reestimate likelihood parameters? Tree topology will not be optimized. # (recommanded) optimization = FullD(derivatives=Newton) # Tell if the parameter should be transformed in order to remove constraints. # This can improves the optimization, but might be a bit slower. optimization.reparametrization = no # Final optimization step, may be useful if numerical derivatives are used: # powell or simplex or none. optimization.final = none # Set the quantity of output to the screen: optimization.verbose = 3 # Parameters to ignore (for instance equilibrium frequencies) optimization.ignore_parameters = # Maximum number of likelihood evaluations: optimization.max_number_f_eval = 10000 # Precision to reach: optimization.tolerance = 0.000001 # idem for error or warning messages: optimization.message_handler = $(DATA).messages # A file where to dump optimization steps (a file path or std for standard output) optimization.profiler = $(DATA).profile # Shall we optimize tree topology as well? optimization.topology = no # Algorithm to use for topology estimation: only NNI for now optimization.topology.algorithm = NNI # NNI method: fast, better or phyml # You should use the phyml option, since it is really more efficient! optimization.topology.algorithm_nni.method = phyml # Number of phyml topology movement steps before reoptimizing parameters: optimization.topology.nstep = 4 # Shall we estimate parameters before looking for topology movements? optimization.topology.numfirst = no # Tolerances: These numbers should not be too low, in order to save computation # time and also for a better topology estimation. # The optimization.tolerance parameter will be used for the final optimization # of numerical parameters. # # Tolerance for the prior-topology estimation optimization.topology.tolerance.before = 100 # Tolerance for the during-topology estimation optimization.topology.tolerance.during = 100 # Shall we first scale the tree before optimizing parameters? [deprecated] optimization.scale_first = no # Should we write the resulting tree? none or file name. output.tree.file = $(DATA).ML.dnd output.tree.format = Newick # Alignment information log file (site specific rates, etc): output.infos = $(DATA).infos # Write numerical parameter estimated values: output.estimates = $(DATA).params.txt # ---------------------------------------------------------------------------------------- # Bootstrap # ---------------------------------------------------------------------------------------- bootstrap.number = 0 # Tell if numerical parameters should be kept to their initial value when bootstrapping: bootstrap.approximate = no # Set this to yes for detailed output when bootstrapping. bootstrap.verbose = no bootstrap.output.file = $(DATA).ML_bstrees.dnd bppsuite-2.4.1/Examples/MaximumLikelihood/Codons/M0/000077500000000000000000000000001333524216000222505ustar00rootroot00000000000000bppsuite-2.4.1/Examples/MaximumLikelihood/Codons/M0/ML.bpp000066400000000000000000000127631333524216000232740ustar00rootroot00000000000000#Example data set adapted from PAML # #logL0 = -1084.23740828789 #logL = -1056.00142355909 # Global variables: DATA = lysozymeLarge # Sequences: # The alphabet to use: # DNA, RNA or Protein... alphabet=Codon(letter=DNA) genetic_code=Standard # The sequence file to use (sequences must be aligned!) input.sequence.file=../../../Data/$(DATA).fasta # The alignment format: input.sequence.format=Fasta #Sites to use: # all, nogap or complete (=only resolved chars) input.sequence.sites_to_use = all # Specify a maximum amount of gaps: may be an absolute number or a percentage. input.sequence.max_gap_allowed = 50% input.sequence.remove_stop_codons = yes # ---------------------------------------------------------------------------------------- # Input tree file # ---------------------------------------------------------------------------------------- # user or random init.tree = user input.tree.file = ../../../Data/$(DATA).dnd input.tree.format = Newick init.brlen.method = Input # ---------------------------------------------------------------------------------------- # Model specification # ---------------------------------------------------------------------------------------- # See the manual for a description of the syntax and available options. # model = YN98(kappa=1, omega=1.0, frequencies=F0) nonhomogeneous = no rate_distribution = Constant() //Gamma(n=4, alpha=0.358) # Likelihood recursion option: # - simple: derivatives takes more time to compute, but likelihood computation is faster. # For big data sets, it can save a lot of memory usage too, particularly when the data are compressed. # - double: Uses more memory and need more time to compute likelihood, due to the double recursion. # Analytical derivatives are however faster to compute. # This option has no effect in the following cases: # - Topology estimation: this requires a double recursive algorithm, # - Optimization with a molecular clock: a simple recursion with data compression is used in this case, # due to the impossibility of computing analytical derivatives. likelihood.recursion = simple # Site compression for the simple recursion: # - simple: identical sites are not computed twice # - recursive: look for site patterns to save computation time during optimization, but # requires extra time for building the patterns. # This is usually the best option, particularly for nucleotide data sets. likelihood.recursion_simple.compression = recursive # ---------------------------------------------------------------------------------------- # Optimization # ---------------------------------------------------------------------------------------- # Should we reestimate likelihood parameters? Tree topology will not be optimized. # (recommanded) optimization = FullD(derivatives=Newton) # Tell if the parameter should be transformed in order to remove constraints. # This can improves the optimization, but might be a bit slower. optimization.reparametrization = no # Final optimization step, may be useful if numerical derivatives are used: # powell or simplex or none. optimization.final = none # Set the quantity of output to the screen: optimization.verbose = 3 # Parameters to ignore (for instance equilibrium frequencies) optimization.ignore_parameters = # Maximum number of likelihood evaluations: optimization.max_number_f_eval = 10000 # Precision to reach: optimization.tolerance = 0.000001 # idem for error or warning messages: optimization.message_handler = $(DATA).messages # A file where to dump optimization steps (a file path or std for standard output) optimization.profiler = $(DATA).profile # Shall we optimize tree topology as well? optimization.topology = no # Algorithm to use for topology estimation: only NNI for now optimization.topology.algorithm = NNI # NNI method: fast, better or phyml # You should use the phyml option, since it is really more efficient! optimization.topology.algorithm_nni.method = phyml # Number of phyml topology movement steps before reoptimizing parameters: optimization.topology.nstep = 4 # Shall we estimate parameters before looking for topology movements? optimization.topology.numfirst = no # Tolerances: These numbers should not be too low, in order to save computation # time and also for a better topology estimation. # The optimization.tolerance parameter will be used for the final optimization # of numerical parameters. # # Tolerance for the prior-topology estimation optimization.topology.tolerance.before = 100 # Tolerance for the during-topology estimation optimization.topology.tolerance.during = 100 # Shall we first scale the tree before optimizing parameters? [deprecated] optimization.scale_first = no # Should we write the resulting tree? none or file name. output.tree.file = $(DATA).ML.dnd output.tree.format = Newick # Alignment information log file (site specific rates, etc): output.infos = $(DATA).infos # Write numerical parameter estimated values: output.estimates = $(DATA).params.txt # ---------------------------------------------------------------------------------------- # Bootstrap # ---------------------------------------------------------------------------------------- bootstrap.number = 0 # Tell if numerical parameters should be kept to their initial value when bootstrapping: bootstrap.approximate = no # Set this to yes for detailed output when bootstrapping. bootstrap.verbose = no bootstrap.output.file = $(DATA).ML_bstrees.dnd bppsuite-2.4.1/Examples/MaximumLikelihood/Codons/M1/000077500000000000000000000000001333524216000222515ustar00rootroot00000000000000bppsuite-2.4.1/Examples/MaximumLikelihood/Codons/M1/ML.bpp000066400000000000000000000131371333524216000232710ustar00rootroot00000000000000#Example data set adapted from PAML # #Initial log likelihood.................: -1069.68587126864 # Global variables: DATA = lysozymeLarge # Sequences: # The alphabet to use: # DNA, RNA or Protein... alphabet=Codon(letter=DNA, type=Standard) # The sequence file to use (sequences must be aligned!) input.sequence.file=../../../Data/$(DATA).fasta # The alignment format: input.sequence.format=Fasta #Sites to use: # all, nogap or complete (=only resolved chars) input.sequence.sites_to_use = all # Specify a maximum amount of gaps: may be an absolute number or a percentage. input.sequence.max_gap_allowed = 50% input.sequence.max_unresolved_allowed = 50% input.sequence.remove_stop_codons = yes # ---------------------------------------------------------------------------------------- # Input tree file # ---------------------------------------------------------------------------------------- # user or random init.tree = user input.tree.file = ../../../Data/$(DATA).dnd input.tree.format = Newick init.brlen.method = Input # ---------------------------------------------------------------------------------------- # Model specification # ---------------------------------------------------------------------------------------- # See the manual for a description of the syntax and available options. # model = YNGP_M1(kappa=1, omega=0.5, frequencies=F1X4, p0=0.5, initFreqs=observed, observedPseudoCount=1) nonhomogeneous=no rate_distribution = Constant //Gamma(n=4, alpha=0.358) # Likelihood recursion option: # - simple: derivatives takes more time to compute, but likelihood computation is faster. # For big data sets, it can save a lot of memory usage too, particularly when the data are compressed. # - double: Uses more memory and need more time to compute likelihood, due to the double recursion. # Analytical derivatives are however faster to compute. # This option has no effect in the following cases: # - Topology estimation: this requires a double recursive algorithm, # - Optimization with a molecular clock: a simple recursion with data compression is used in this case, # due to the impossibility of computing analytical derivatives. likelihood.recursion = simple # Site compression for the simple recursion: # - simple: identical sites are not computed twice # - recursive: look for site patterns to save computation time during optimization, but # requires extra time for building the patterns. # This is usually the best option, particularly for nucleotide data sets. likelihood.recursion_simple.compression = recursive # ---------------------------------------------------------------------------------------- # Optimization # ---------------------------------------------------------------------------------------- # Should we reestimate likelihood parameters? Tree topology will not be optimized. # (recommanded) optimization = FullD(derivatives=Newton) # Tell if the parameter should be transformed in order to remove constraints. # This can improves the optimization, but might be a bit slower. optimization.reparametrization = no # Final optimization step, may be useful if numerical derivatives are used: # powell or simplex or none. optimization.final = none # Set the quantity of output to the screen: optimization.verbose = 3 # Parameters to ignore (for instance equilibrium frequencies) optimization.ignore_parameters = YNGP_M1.*Full* # Maximum number of likelihood evaluations: optimization.max_number_f_eval = 10000 # Precision to reach: optimization.tolerance = 0.000001 # idem for error or warning messages: optimization.message_handler = $(DATA).messages # A file where to dump optimization steps (a file path or std for standard output) optimization.profiler = $(DATA).profile # Shall we optimize tree topology as well? optimization.topology = no # Algorithm to use for topology estimation: only NNI for now optimization.topology.algorithm = NNI # NNI method: fast, better or phyml # You should use the phyml option, since it is really more efficient! optimization.topology.algorithm_nni.method = phyml # Number of phyml topology movement steps before reoptimizing parameters: optimization.topology.nstep = 4 # Shall we estimate parameters before looking for topology movements? optimization.topology.numfirst = no # Tolerances: These numbers should not be too low, in order to save computation # time and also for a better topology estimation. # The optimization.tolerance parameter will be used for the final optimization # of numerical parameters. # # Tolerance for the prior-topology estimation optimization.topology.tolerance.before = 100 # Tolerance for the during-topology estimation optimization.topology.tolerance.during = 100 # Shall we first scale the tree before optimizing parameters? [deprecated] optimization.scale_first = no # Should we write the resulting tree? none or file name. output.tree.file = $(DATA).ML.dnd output.tree.format = Newick # Alignment information log file (site specific rates, etc): output.infos = $(DATA).infos # Write numerical parameter estimated values: output.estimates = $(DATA).params.txt # ---------------------------------------------------------------------------------------- # Bootstrap # ---------------------------------------------------------------------------------------- bootstrap.number = 0 # Tell if numerical parameters should be kept to their initial value when bootstrapping: bootstrap.approximate = no # Set this to yes for detailed output when bootstrapping. bootstrap.verbose = no bootstrap.output.file = $(DATA).ML_bstrees.dnd bppsuite-2.4.1/Examples/MaximumLikelihood/Codons/M2/000077500000000000000000000000001333524216000222525ustar00rootroot00000000000000bppsuite-2.4.1/Examples/MaximumLikelihood/Codons/M2/ML.bpp000066400000000000000000000131141333524216000232650ustar00rootroot00000000000000#Example data set adapted from PAML # #Initial log likelihood.................: -1068.04967173634 # Global variables: DATA = lysozymeLarge # Sequences: # The alphabet to use: # DNA, RNA or Protein... alphabet=Codon(letter=DNA, type=Standard) # The sequence file to use (sequences must be aligned!) input.sequence.file=../../../Data/$(DATA).fasta # The alignment format: input.sequence.format=Fasta #Sites to use: # all, nogap or complete (=only resolved chars) input.sequence.sites_to_use = all # Specify a maximum amount of gaps: may be an absolute number or a percentage. input.sequence.max_gap_allowed = 50% input.sequence.remove_stop_codons = yes # ---------------------------------------------------------------------------------------- # Input tree file # ---------------------------------------------------------------------------------------- # user or random init.tree = user input.tree.file = ../../../Data/$(DATA).dnd input.tree.format = Newick init.brlen.method = Input # ---------------------------------------------------------------------------------------- # Model specification # ---------------------------------------------------------------------------------------- # See the manual for a description of the syntax and available options. # model = YNGP_M2(kappa=1, omega0=0.5, omega2=2.0, frequencies=F3X4, theta1=0.33333, theta2=0.5, initFreqs=observed) nonhomogeneous=no rate_distribution = Constant() //Gamma(n=4, alpha=0.358) # Likelihood recursion option: # - simple: derivatives takes more time to compute, but likelihood computation is faster. # For big data sets, it can save a lot of memory usage too, particularly when the data are compressed. # - double: Uses more memory and need more time to compute likelihood, due to the double recursion. # Analytical derivatives are however faster to compute. # This option has no effect in the following cases: # - Topology estimation: this requires a double recursive algorithm, # - Optimization with a molecular clock: a simple recursion with data compression is used in this case, # due to the impossibility of computing analytical derivatives. likelihood.recursion = simple # Site compression for the simple recursion: # - simple: identical sites are not computed twice # - recursive: look for site patterns to save computation time during optimization, but # requires extra time for building the patterns. # This is usually the best option, particularly for nucleotide data sets. likelihood.recursion_simple.compression = recursive # ---------------------------------------------------------------------------------------- # Optimization # ---------------------------------------------------------------------------------------- # Should we reestimate likelihood parameters? Tree topology will not be optimized. # (recommanded) optimization = D-Brent(derivatives=Newton, nstep=10) # Tell if the parameter should be transformed in order to remove constraints. # This can improves the optimization, but might be a bit slower. optimization.reparametrization = no # Final optimization step, may be useful if numerical derivatives are used: # powell or simplex or none. optimization.final = none # Set the quantity of output to the screen: optimization.verbose = 3 # Parameters to ignore (for instance equilibrium frequencies) optimization.ignore_parameters = YNGP_M1.*Full* # Maximum number of likelihood evaluations: optimization.max_number_f_eval = 10000 # Precision to reach: optimization.tolerance = 0.000001 # idem for error or warning messages: optimization.message_handler = $(DATA).messages # A file where to dump optimization steps (a file path or std for standard output) optimization.profiler = $(DATA).profile # Shall we optimize tree topology as well? optimization.topology = no # Algorithm to use for topology estimation: only NNI for now optimization.topology.algorithm = NNI # NNI method: fast, better or phyml # You should use the phyml option, since it is really more efficient! optimization.topology.algorithm_nni.method = phyml # Number of phyml topology movement steps before reoptimizing parameters: optimization.topology.nstep = 4 # Shall we estimate parameters before looking for topology movements? optimization.topology.numfirst = no # Tolerances: These numbers should not be too low, in order to save computation # time and also for a better topology estimation. # The optimization.tolerance parameter will be used for the final optimization # of numerical parameters. # # Tolerance for the prior-topology estimation optimization.topology.tolerance.before = 100 # Tolerance for the during-topology estimation optimization.topology.tolerance.during = 100 # Shall we first scale the tree before optimizing parameters? [deprecated] optimization.scale_first = no # Should we write the resulting tree? none or file name. output.tree.file = $(DATA).ML.dnd output.tree.format = Newick # Alignment information log file (site specific rates, etc): output.infos = $(DATA).infos # Write numerical parameter estimated values: output.estimates = $(DATA).params.txt # ---------------------------------------------------------------------------------------- # Bootstrap # ---------------------------------------------------------------------------------------- bootstrap.number = 0 # Tell if numerical parameters should be kept to their initial value when bootstrapping: bootstrap.approximate = no # Set this to yes for detailed output when bootstrapping. bootstrap.verbose = no bootstrap.output.file = $(DATA).ML_bstrees.dnd bppsuite-2.4.1/Examples/MaximumLikelihood/Nucleotides/000077500000000000000000000000001333524216000230255ustar00rootroot00000000000000bppsuite-2.4.1/Examples/MaximumLikelihood/Nucleotides/Homogeneous/000077500000000000000000000000001333524216000253155ustar00rootroot00000000000000bppsuite-2.4.1/Examples/MaximumLikelihood/Nucleotides/Homogeneous/Ancestor.bpp000066400000000000000000000035431333524216000276030ustar00rootroot00000000000000# WARNING!!! You need to run bppml on the ML.bpp example file first to be able to run this example! # Global variables: DATA = LSU # Sequences: # The alphabet to use: # DNA, RNA or Protein alphabet=DNA # The sequence file to use (sequences must be aligned!) input.sequence.file=../../../Data/$(DATA).phy # The alignment format: input.sequence.format=Phylip(order=sequential, type=extended) #Sites to use: # all, nogap or complete (=only resolved chars) input.sequence.sites_to_use = complete # Specify a maximum amount of gaps: may be an absolute number or a percentage. input.sequence.max_gap_allowed = 100% input.tree.file = $(DATA).ML.dnd input.tree.format = Newick # ---------------------------------------------------------------------------------------- # Model specification # ---------------------------------------------------------------------------------------- # the same syntax as in bppML! # Here we directly use the output file from example ML.bpp to load the model: param = LSU.params.txt # ---------------------------------------------------------------------------------------- # Ancestral Sequence Reconstruction # ---------------------------------------------------------------------------------------- asr.method = marginal //only option for now # Shall we output the site specific probabilities in each case: asr.probabilities = yes # Should we sample from the posterior distribution instead of using the maximum probability? asr.sample = yes # How many samples should we use? asr.sample.number = 10 # Alignment information log file (site specific rates, probabilities, etc): output.sites.file = $(DATA).sites.csv # Nodes information log file output.nodes.file = $(DATA).nodes.csv # Write sequences: output.sequence.file = $(DATA).ancestors.fasta output.sequence.format = Fasta bppsuite-2.4.1/Examples/MaximumLikelihood/Nucleotides/Homogeneous/ML.bpp000066400000000000000000000132731333524216000263360ustar00rootroot00000000000000#initial logL: -65826.8571771722 #final logL: -65428.449112789 # Global variables: DATA = LSU # Sequences: # The alphabet to use: # DNA, RNA or Protein alphabet=DNA # The sequence file to use (sequences must be aligned!) input.sequence.file=../../../Data/$(DATA).phy # The alignment format: input.sequence.format=Phylip(order=sequential, type=extended, split=spaces) #Sites to use: # all, nogap or complete (=only resolved chars) input.sequence.sites_to_use = all # Specify a maximum amount of gaps: may be an absolute number or a percentage. input.sequence.max_gap_allowed = 50% input.sequence.max_unresolved_allowed = 100% # ---------------------------------------------------------------------------------------- # Input tree file # ---------------------------------------------------------------------------------------- # user or random init.tree = user input.tree.file = ../../../Data/$(DATA).dnd input.tree.format = Newick init.brlen.method = Input # ---------------------------------------------------------------------------------------- # Model specification # ---------------------------------------------------------------------------------------- # See the manual for a description of the syntax and available options. # model = HKY85(kappa=2.843, initFreqs=observed) rate_distribution = Gamma(n=4, alpha=0.358) # Likelihood recursion option: # - simple: derivatives takes more time to compute, but likelihood computation is faster. # For big data sets, it can save a lot of memory usage too, particularly when the data are compressed. # - double: Uses more memory and need more time to compute likelihood, due to the double recursion. # Analytical derivatives are however faster to compute. # This option has no effect in the following cases: # - Topology estimation: this requires a double recursive algorithm, # - Optimization with a molecular clock: a simple recursion with data compression is used in this case, # due to the impossibility of computing analytical derivatives. likelihood.recursion = simple # Site compression for the simple recursion: # - simple: identical sites are not computed twice # - recursive: look for site patterns to save computation time during optimization, but # requires extra time for building the patterns. # This is usually the best option, particularly for nucleotide data sets. likelihood.recursion_simple.compression = recursive # ---------------------------------------------------------------------------------------- # Optimization # ---------------------------------------------------------------------------------------- # Should we reestimate likelihood parameters? Tree topology will not be optimized. # (recommanded) # Method to use for optimizing numerical parameters: # - None, no optimization performed # - DB derivatives for branch lengths + Brent for other parameters # - FullD derivatives for all parameters, using numerical derivatives for non-branch lengths parameters. optimization = FullD(derivatives=Newton) # Tell if the parameter should be transformed in order to remove constraints. # This can improves the optimization, but might be a bit slower. optimization.reparametrization = no # Final optimization step, may be useful if numerical derivatives are used: # powell or simplex or none. optimization.final = none # Set the quantity of output to the screen: optimization.verbose = 3 # Parameters to ignore (for instance equilibrium frequencies) optimization.ignore_parameters = # Maximum number of likelihood evaluations: optimization.max_number_f_eval = 10000 # Precision to reach: optimization.tolerance = 0.000001 # idem for error or warning messages: optimization.message_handler = $(DATA).messages # A file where to dump optimization steps (a file path or std for standard output) optimization.profiler = $(DATA).profile # Shall we optimize tree topology as well? optimization.topology = yes # Algorithm to use for topology estimation: only NNI for now optimization.topology.algorithm = NNI # NNI method: fast, better or phyml # You should use the phyml option, since it is really more efficient! optimization.topology.algorithm_nni.method = phyml # Number of phyml topology movement steps before reoptimizing parameters: optimization.topology.nstep = 4 # Shall we estimate parameters before looking for topology movements? optimization.topology.numfirst = no # Tolerances: These numbers should not be too low, in order to save computation # time and also for a better topology estimation. # The optimization.tolerance parameter will be used for the final optimization # of numerical parameters. # # Tolerance for the prior-topology estimation optimization.topology.tolerance.before = 100 # Tolerance for the during-topology estimation optimization.topology.tolerance.during = 100 # Shall we first scale the tree before optimizing parameters? [deprecated] optimization.scale_first = no # Should we write the resulting tree? none or file name. output.tree.file = $(DATA).ML.dnd output.tree.format = Newick # Alignment information log file (site specific rates, etc): output.infos = $(DATA).infos # Write numerical parameter estimated values: output.estimates = $(DATA).params.txt # ---------------------------------------------------------------------------------------- # Bootstrap # ---------------------------------------------------------------------------------------- bootstrap.number = 0 # Tell if numerical parameters should be kept to their initial value when bootstrapping: bootstrap.approximate = no # Set this to yes for detailed output when bootstrapping. bootstrap.verbose = no bootstrap.output.file = $(DATA).ML_bstrees.dnd bppsuite-2.4.1/Examples/MaximumLikelihood/Nucleotides/NonHomogeneousGG/000077500000000000000000000000001333524216000262065ustar00rootroot00000000000000bppsuite-2.4.1/Examples/MaximumLikelihood/Nucleotides/NonHomogeneousGG/MLNHGG.bpp000066400000000000000000000107061333524216000276710ustar00rootroot00000000000000#Initial log likelihood.................: -65639.1410465442 #Log likelihood.........................: -64547.3486924172 #GC.theta...............................: 0.486755 #T92.theta_1............................: 0.438231 #T92.theta_2............................: 0.778332 #etc #Gamma.alpha............................: 0.436095 #2621.12user 0.63system 43:47.81elapsed 99%CPU # Global variables: DATA = LSU # Sequences: # The alphabet to use: # DNA, RNA or Protein alphabet=DNA # The sequence file to use (sequences must be aligned!) input.sequence.file=../../../Data/$(DATA).phy # The alignment format: input.sequence.format=Phylip(order=sequential, type=extended) #Sites to use: # all, nogap or complete (=only resolved chars) input.sequence.sites_to_use = complete # Specify a maximum amount of gaps: may be an absolute number or a percentage. input.sequence.max_gap_allowed = 100% # ---------------------------------------------------------------------------------------- # Input tree file # ---------------------------------------------------------------------------------------- # user or random init.tree = user input.tree.file = ../../../Data/$(DATA).dnd input.tree.format = Newick init.brlen.method = Input # ---------------------------------------------------------------------------------------- # Model specification # ---------------------------------------------------------------------------------------- # See the manual for a description of the syntax and available options. # # Homogeneous model? # no => Homogeneous case # one_per_branch => Galtier & Gouy 97 series of NH models # general => Specify the model by hand. nonhomogeneous = one_per_branch # Options for non-homogeneous one-per_branch models: model = T92(kappa=2.843, theta=0.5) # For one_per_branch heterogeneous models. # Tell which parameters are common to all branches. # Other parameters will be considered branch specific. nonhomogeneous_one_per_branch.shared_parameters = T92.kappa nonhomogeneous.root_freq = GC(init=balanced) rate_distribution = Gamma(n=4, alpha=0.358) # Likelihood recursion option: # - simple: derivatives takes more time to compute, but likelihooh computation is faster. # For big data sets, it can save a lot of memory usage too, particularly when the data are compressed. # - double: Uses more memory and need more time to compute likelihood, due to the double recursion. # Analytical derivatives are however faster to compute. likelihood.recursion = simple # Site compression for the simple recursion: # - simple: identical sites are not computed twice # - recursive: look for site patterns to save computation time during optimization, but # requires extra time for building the patterns. # This is usually the best option, particularly for nucleotides data sets. likelihood.recursion_simple.compression = recursive # ---------------------------------------------------------------------------------------- # Optimization # ---------------------------------------------------------------------------------------- optimization=FullD(derivatives=Newton) optimization.reparametrization=no optimization.verbose = 1 optimization.ignore_parameter = optimization.max_number_f_eval = 10000 optimization.tolerance = 0.000001 optimization.message_handler = $(DATA).messages optimization.profiler = $(DATA).profile optimization.backup.file = .$(DATA).bck optimization.topology = no optimization.topology.nstep=4 optimization.topology.numfirst=no optimization.topology.tolerance.before=100 optimization.topology.tolerance.during=100 optimization.scale_first=no optimization.verbose=3 optimization.ignore_parameters= # Should we write the resulting tree? none or file name. output.tree.file = $(DATA).ML.dnd output.tree.format = Newick # Alignment information log file (site specific rates, etc): output.infos = $(DATA).infos # Write numerical parameter estimated values: output.estimates = $(DATA).params.txt # ---------------------------------------------------------------------------------------- # Bootstrap # ---------------------------------------------------------------------------------------- bootstrap.number = 0 # Tell if numerical parameters should be kept to their initial value when bootstrapping: bootstrap.approximate = no # Set this to yes for detailed output when bootstrapping. bootstrap.verbose = no bootstrap.output.file = $(DATA).ML_bstrees.dnd bppsuite-2.4.1/Examples/MaximumLikelihood/Nucleotides/NonHomogeneousGeneral/000077500000000000000000000000001333524216000272665ustar00rootroot00000000000000bppsuite-2.4.1/Examples/MaximumLikelihood/Nucleotides/NonHomogeneousGeneral/Ancestor.bpp000066400000000000000000000035431333524216000315540ustar00rootroot00000000000000# WARNING!!! You need to run bppml on the ML.bpp example file first to be able to run this example! # Global variables: DATA = LSU # Sequences: # The alphabet to use: # DNA, RNA or Protein alphabet=DNA # The sequence file to use (sequences must be aligned!) input.sequence.file=../../../Data/$(DATA).phy # The alignment format: input.sequence.format=Phylip(order=sequential, type=extended) #Sites to use: # all, nogap or complete (=only resolved chars) input.sequence.sites_to_use = complete # Specify a maximum amount of gaps: may be an absolute number or a percentage. input.sequence.max_gap_allowed = 100% input.tree.file = $(DATA).ML.dnd input.tree.format = Newick # ---------------------------------------------------------------------------------------- # Model specification # ---------------------------------------------------------------------------------------- # the same syntax as in bppML! # Here we directly use the output file from example ML.bpp to load the model: param = LSU.params.txt # ---------------------------------------------------------------------------------------- # Ancestral Sequence Reconstruction # ---------------------------------------------------------------------------------------- asr.method = marginal //only option for now # Shall we output the site specific probabilities in each case: asr.probabilities = yes # Should we sample from the posterior distribution instead of using the maximum probability? asr.sample = yes # How many samples should we use? asr.sample.number = 10 # Alignment information log file (site specific rates, probabilities, etc): output.sites.file = $(DATA).sites.csv # Nodes information log file output.nodes.file = $(DATA).nodes.csv # Write sequences: output.sequence.file = $(DATA).ancestors.fasta output.sequence.format = Fasta bppsuite-2.4.1/Examples/MaximumLikelihood/Nucleotides/NonHomogeneousGeneral/MLNH.bpp000066400000000000000000000117141333524216000305330ustar00rootroot00000000000000#Initial log likelihood.................: -67066.6981049241 #Log likelihood.........................: -65187.3822910926 #Full.theta.............................: 0.481587 #Full.theta1............................: 0.568231 #Full.theta2............................: 0.591547 #GTR.a_1................................: 1.27372 #GTR.b_1................................: 0.667001 #GTR.c_1................................: 0.344267 #GTR.d_1................................: 0.339924 #GTR.e_1................................: 0.37557 #GTR.theta_1............................: 0.622987 #GTR.theta1_1...........................: 0.469133 #GTR.theta2_1...........................: 0.547965 #GTR.theta_2............................: 0.491549 #GTR.theta1_2...........................: 0.485613 #GTR.theta2_2...........................: 0.555095 #Gamma.alpha............................: 0.438647 # Global variables: DATA = LSU # Sequences: # The alphabet to use: # DNA, RNA or Protein alphabet=DNA # The sequence file to use (sequences must be aligned!) input.sequence.file=../../../Data/$(DATA).phy # The alignment format: input.sequence.format=Phylip(order=sequential, type=extended) #Sites to use: # all, nogap or complete (=only resolved chars) input.sequence.sites_to_use = complete # Specify a maximum amount of gaps: may be an absolute number or a percentage. input.sequence.max_gap_allowed = 100% # ---------------------------------------------------------------------------------------- # Input tree file # ---------------------------------------------------------------------------------------- # user or random init.tree = user input.tree.file = ../../../Data/$(DATA).dnd input.tree.format = Newick init.brlen.method = Input # ---------------------------------------------------------------------------------------- # Model specification # ---------------------------------------------------------------------------------------- # Homogeneous model? # no => Homogeneous case # one_per_branch => Galtier & Gouy 97 series of NH models # general => Specify the model by hand. nonhomogeneous = general nonhomogeneous.root_freq=Full(init=balanced) rate_distribution = Gamma(n=4, alpha=0.358) # Now the general heterogeneous case: # Specify the number of distincts models. nonhomogeneous.number_of_models = 2 # Set up each model: model1 = GTR(initFreqs=observed) model1.nodes_id=0:62 # The Ids of the nodes to which this model should be assigned. model2 = GTR(a=model1.GTR.a,\ b=model1.GTR.b,\ c=model1.GTR.c,\ d=model1.GTR.d,\ e=model1.GTR.e,\ initFreqs=observed) model2.nodes_id=63:154 # Likelihood recursion option: # - simple: derivatives takes more time to compute, but likelihooh computation is faster. # For big data sets, it can save a lot of memory usage too, particularly when the data are compressed. # - double: Uses more memory and need more time to compute likelihood, due to the double recursion. # Analytical derivatives are however faster to compute. likelihood.recursion = simple # Site compression for the simple recursion: # - simple: identical sites are not computed twice # - recursive: look for site patterns to save computation time during optimization, but # requires extra time for building the patterns. # This is usually the best option, particularly for nucleotides data sets. likelihood.recursion_simple.compression = recursive # ---------------------------------------------------------------------------------------- # Optimization # ---------------------------------------------------------------------------------------- optimization=FullD(derivatives=Newton) optimization.reparametrization=no optimization.verbose = 1 optimization.ignore_parameters = optimization.max_number_f_eval = 10000 optimization.tolerance = 0.000001 optimization.message_handler = $(DATA).messages optimization.profiler = $(DATA).profile optimization.topology = no optimization.topology.nstep=4 optimization.topology.numfirst=no optimization.topology.tolerance.before=100 optimization.topology.tolerance.during=100 optimization.scale_first=no optimization.verbose=3 # Should we write the resulting tree? none or file name. output.tree.file = $(DATA).ML.dnd output.tree.format = Newick # Alignment information log file (site specific rates, etc): output.infos = $(DATA).infos # Write numerical parameter estimated values: output.estimates = $(DATA).params.txt # ---------------------------------------------------------------------------------------- # Bootstrap # ---------------------------------------------------------------------------------------- bootstrap.number = 0 # Tell if numerical parameters should be kept to their initial value when bootstrapping: bootstrap.approximate = no # Set this to yes for detailed output when bootstrapping. bootstrap.verbose = no bootstrap.output.file = $(DATA).ML_bstrees.dnd bppsuite-2.4.1/Examples/MaximumLikelihood/Proteins/000077500000000000000000000000001333524216000223525ustar00rootroot00000000000000bppsuite-2.4.1/Examples/MaximumLikelihood/Proteins/Homogeneous/000077500000000000000000000000001333524216000246425ustar00rootroot00000000000000bppsuite-2.4.1/Examples/MaximumLikelihood/Proteins/Homogeneous/Ancestor.bpp000066400000000000000000000036051333524216000271270ustar00rootroot00000000000000# WARNING!!! You need to run bppml on the ML.bpp example file first to be able to run this example! # Global variables: DATA = Myo # Sequences: # The alphabet to use: # DNA, RNA or Protein alphabet=Protein # The sequence file to use (sequences must be aligned!) input.sequence.file=../../../Data/$(DATA).mase # The alignment format: input.sequence.format=Mase #Sites to use: # all, nogap or complete (=only resolved chars) input.sequence.sites_to_use = all # Specify a maximum amount of gaps: may be an absolute number or a percentage. input.sequence.max_gap_allowed = 100% input.tree.file = $(DATA).ML.dnd input.tree.format = Newick # ---------------------------------------------------------------------------------------- # Model specification # ---------------------------------------------------------------------------------------- # the same syntax as in bppML! # Here we directly use the output file from example ML.bpp to load the model: param = Myo.params.txt # ---------------------------------------------------------------------------------------- # Ancestral Sequence Reconstruction # ---------------------------------------------------------------------------------------- asr.method = marginal //only option for now # Shall we output the site specific probabilities in each case: asr.probabilities = yes # Should we sample from the posterior distribution instead of using the maximum probability? asr.sample = no # How many samples should we use? asr.sample.number = 10 # Shall we add extant sequences to output file? asr.add_extant = yes # Alignment information log file (site specific rates, probabilities, etc): output.sites.file = $(DATA).sites.csv # Nodes information log file output.nodes.file = $(DATA).nodes.csv # Write sequences: output.sequence.file = $(DATA).ancestors.fasta output.sequence.format = Fasta bppsuite-2.4.1/Examples/MaximumLikelihood/Proteins/Homogeneous/ML.bpp000066400000000000000000000132001333524216000256510ustar00rootroot00000000000000#initial logL: -5140.62856257665 #final logL: -4958.52926533168 # Global variables: DATA = Myo # Sequences: # The alphabet to use: # DNA, RNA or Protein alphabet=Protein # The sequence file to use (sequences must be aligned!) input.sequence.file=../../../Data/$(DATA).mase # The alignment format: input.sequence.format=Mase #Sites to use: # all, nogap or complete (=only resolved chars) input.sequence.sites_to_use = all # Specify a maximum amount of gaps: may be an absolute number or a percentage. input.sequence.max_gap_allowed = 50% # ---------------------------------------------------------------------------------------- # Input tree file # ---------------------------------------------------------------------------------------- # user or random init.tree = user input.tree.file = ../../../Data/$(DATA).dnd input.tree.format = Newick init.brlen.method = Input # ---------------------------------------------------------------------------------------- # Model specification # ---------------------------------------------------------------------------------------- # See the manual for a description of the syntax and available options. # model = JTT92 //JTT92+F(initFreqs=observed, initFreqs.observedPseudoCount=0.) rate_distribution = Gamma(n=4, alpha=0.5) # Likelihood recursion option: # - simple: derivatives takes more time to compute, but likelihood computation is faster. # For big data sets, it can save a lot of memory usage too, particularly when the data are compressed. # - double: Uses more memory and need more time to compute likelihood, due to the double recursion. # Analytical derivatives are however faster to compute. # This option has no effect in the following cases: # - Topology estimation: this requires a double recursive algorithm, # - Optimization with a molecular clock: a simple recursion with data compression is used in this case, # due to the impossibility of computing analytical derivatives. likelihood.recursion = simple # Site compression for the simple recursion: # - simple: identical sites are not computed twice # - recursive: look for site patterns to save computation time during optimization, but # requires extra time for building the patterns. # This is usually the best option, particularly for nucleotide data sets. likelihood.recursion_simple.compression = recursive # ---------------------------------------------------------------------------------------- # Optimization # ---------------------------------------------------------------------------------------- # Should we reestimate likelihood parameters? Tree topology will not be optimized. # (recommanded) # Method to use for optimizing numerical parameters: # - None, no optimization performed # - DB derivatives for branch lengths + Brent for other parameters # - FullD derivatives for all parameters, using numerical derivatives for non-branch lengths parameters. optimization = FullD(derivatives=Newton) # Tell if the parameter should be transformed in order to remove constraints. # This can improves the optimization, but might be a bit slower. optimization.reparametrization = no # Final optimization step, may be useful if numerical derivatives are used: # powell or simplex or none. optimization.final = none # Set the quantity of output to the screen: optimization.verbose = 3 # Parameters to ignore (for instance equilibrium frequencies) optimization.ignore_parameters = # Maximum number of likelihood evaluations: optimization.max_number_f_eval = 10000 # Precision to reach: optimization.tolerance = 0.000001 # idem for error or warning messages: optimization.message_handler = $(DATA).messages # A file where to dump optimization steps (a file path or std for standard output) optimization.profiler = $(DATA).profile # Shall we optimize tree topology as well? optimization.topology = yes # Algorithm to use for topology estimation: only NNI for now optimization.topology.algorithm = NNI # NNI method: fast, better or phyml # You should use the phyml option, since it is really more efficient! optimization.topology.algorithm_nni.method = phyml # Number of phyml topology movement steps before reoptimizing parameters: optimization.topology.nstep = 4 # Shall we estimate parameters before looking for topology movements? optimization.topology.numfirst = no # Tolerances: These numbers should not be too low, in order to save computation # time and also for a better topology estimation. # The optimization.tolerance parameter will be used for the final optimization # of numerical parameters. # # Tolerance for the prior-topology estimation optimization.topology.tolerance.before = 100 # Tolerance for the during-topology estimation optimization.topology.tolerance.during = 100 # Shall we first scale the tree before optimizing parameters? [deprecated] optimization.scale_first = no # Should we write the resulting tree? none or file name. output.tree.file = $(DATA).ML.dnd output.tree.format = Newick # Alignment information log file (site specific rates, etc): output.infos = $(DATA).infos # Write numerical parameter estimated values: output.estimates = $(DATA).params.txt # ---------------------------------------------------------------------------------------- # Bootstrap # ---------------------------------------------------------------------------------------- bootstrap.number = 0 # Tell if numerical parameters should be kept to their initial value when bootstrapping: bootstrap.approximate = no # Set this to yes for detailed output when bootstrapping. bootstrap.verbose = no bootstrap.output.file = $(DATA).ML_bstrees.dnd bppsuite-2.4.1/Examples/Parsimony/000077500000000000000000000000001333524216000171075ustar00rootroot00000000000000bppsuite-2.4.1/Examples/Parsimony/Pars.bpp000066400000000000000000000014721333524216000205230ustar00rootroot00000000000000# Global variables: DATA = LSU # Sequences: # The laphabet to use: # DNA, RNA or Protein alphabet=DNA use.gaps=no # The sequence file to use (sequences must be aligned!) input.sequence.file=../Data/$(DATA).phy # The alignment format: input.sequence.format=Phylip(order=sequential, type=extended) #Sites to use: # all, nogap or complete (=only resolved chars) input.sequence.sites_to_use = complete # Specify a maximum amount of gaps: may be an absolute number or a percentage. input.sequence.max_gap_allowed = 100% input.tree.file = ../Data/$(DATA).dnd input.tree.format = Newick optimization.topology = yes # Should we write the resulting tree? none or file name. output.tree.file = $(DATA).pars.dnd output.tree.format = Newick # Bootstrap: bootstrap.number = 1000 bootstrap.output.file = $(DATA).pars_bstrees.dnd bppsuite-2.4.1/Examples/PopStats/000077500000000000000000000000001333524216000167035ustar00rootroot00000000000000bppsuite-2.4.1/Examples/PopStats/PopStats.bpp000066400000000000000000000005311333524216000211620ustar00rootroot00000000000000input.sequence.file.ingroup = alignment.phy input.sequence.format.ingroup = Phylip(order=interleaved, type=classic) estimate.kappa = yes pop.stats= \ SiteFrequencies,\ Watterson75,\ Tajima83,\ TajimaD,\ FuAndLiDStar(tot_mut=no),\ FuAndLiFStar(tot_mut=no),\ FuAndLiDStar(tot_mut=yes),\ FuAndLiFStar(tot_mut=yes),\ bppsuite-2.4.1/Examples/PopStats/PopStatsCodonSites.bpp000066400000000000000000000006671333524216000231670ustar00rootroot00000000000000# --------------- # Input sequences # --------------- # The alphabet to use: alphabet=Codon(letter=DNA) genetic_code=Standard # The sequence file to use (sequences must be aligned!) input.sequence.file.ingroup=alignment.phy # The file format: input.sequence.format.ingroup=Phylip(order=interleaved, type=classic) # ---------------- # Analysis # ---------------- pop.stats=CodonSiteStatistics(output.file=alignment.codons.csv),PiN_PiS bppsuite-2.4.1/Examples/PopStats/alignment.phy000066400000000000000000000010051333524216000213770ustar00rootroot00000000000000 10 40 3 TCTGATAGTGACGTCACCGGCGTTTATTACCCTACGTTCA 4 TATGGCAGTGACGTCATCGGCGTCAATTCCCCGACATTCA 9 TATGGCAGTGACGTCATCGGCGTCAATTCCCCGACATTCA 6 TATGGCAGTGACGTCATCGGCGTCAATTCCCCGACATTCA 10 TATGGCAGTGACGTCATCGGCGTCAATTCCCCGACCTTCA 1 TATGGCAGTGACGTCATCGGCGTCAATTCCCCGACCTTCA 5 TATGGCAGTGACGTCATCGGCGTCAATTCCCCGACCTTCA 8 TATGGCAGTGACGTCATCGGCGTCAATTCCCCGACCTTCA 2 GATGGCAGTGACGTCTTCGGCGTCAATTCCCCGACATTGA 7 GATGGCAGTGACGTCTTCGGCGTCAATTCCCCGACATTCA bppsuite-2.4.1/Examples/README000066400000000000000000000033511333524216000160100ustar00rootroot00000000000000 ..:: Data files ::.. Data/ LSU.phy Sequence file in phylip format. LSU.dnd Unrooted tree in newick format. LSUrooted.dnd Rooted tree in newick format. tree.dnd A candidate tree. treeList.dnd A list of trees in newick format. treeList2.dnd Another list of trees in newick format. OutGroup.txt A list of taxons to be used with BppReRoot. lysozymeLarge.fasta and .dnd Files from the PAML package. Myo.mase Myoglobin sequence alignment, From dutheil and Galtier 2007 HIV1_REF_2010_gag_DNA.fasta Alignment file downloaded from the HIV database on 21/12/11 " " _macse realigned with Macse 0.8 ..:: Options files ::.. These option files are split in their respective program directory: Dist.bpp BppDist option file. Pars.bpp BppPars option file. ML.bpp BppML option file. Homogeneous model. MLNHGG.bpp BppML option file. Galtier & Gouy non-homogeneous model, like in the MHNL package. MLNH.bpp BppML option file. Gemeral non-homogeneous models. SeqGen.bpp BppSeqGen option file. SeqGenHomogeneousModel.bpp File included by SeqGen.bpp. Not to be used directly. SeqGenNonHomogeneousModel.bpp File included by SeqGen.bpp. Not to be used directly. Consense.bpp BppConsense option file. SeqMan.bpp BppSeqMan option file. ReRoot.bpp BppReRoot option file. AlnScores.bpp BppAlnscore option file. bppsuite-2.4.1/Examples/ReRooting/000077500000000000000000000000001333524216000170365ustar00rootroot00000000000000bppsuite-2.4.1/Examples/ReRooting/ReRoot.bpp000066400000000000000000000004741333524216000207600ustar00rootroot00000000000000input.list.file = ../Data/treeList2.dnd # [input|consensus] tree = input outgroups.file = ../Data/OutGroup.txt # yes = the unrootable trees are printed as unrooted in the output.tree.file # no = the unrootable trees are not printed in the output.tree.file print.option = no output.trees.file = treeList2_rooted.dnd bppsuite-2.4.1/Examples/SequenceManipulation/000077500000000000000000000000001333524216000212575ustar00rootroot00000000000000bppsuite-2.4.1/Examples/SequenceManipulation/SeqMan.bpp000066400000000000000000000013201333524216000231420ustar00rootroot00000000000000# Global variables: DATA = LSU # --------------- # Input sequences # --------------- # The alphabet to use: # [DNA|RNA|Protein|Generic] alphabet=DNA # The sequence file to use (sequences must be aligned!) input.sequence.file=../Data/$(DATA).phy # The file format: input.sequence.format=Phylip(order=sequential, type=extended) # ---------------- # Output sequences # ---------------- output.sequence.file=$(DATA).fas # The file format: output.sequence.format=Fasta() # ----------------------- # Sequences manipulations # ----------------------- #For example (see manual for a detailed list of available options): sequence.manip = Switch,Transcript,CoerceToAlignment,KeepComplete(maxGapAllowed=30%),GapToUnknown bppsuite-2.4.1/Examples/SequenceManipulation/SeqMan2.bpp000066400000000000000000000013671333524216000232370ustar00rootroot00000000000000# Global variables: DATA = HIV1_REF_2010_gag # --------------- # Input sequences # --------------- # The alphabet to use: # [DNA|RNA|Protein|Generic] alphabet=Codon(code=Standard, letter=DNA) # The sequence file to use (sequences must be aligned!) input.sequence.file=../Data/$(DATA)_DNA.fasta # The file format: input.sequence.format=Fasta # ---------------- # Output sequences # ---------------- output.sequence.file=$(DATA)_AA.fasta # The file format: output.sequence.format=Fasta() # ----------------------- # Sequences manipulations # ----------------------- #For example (see manual for a detailed list of available options): sequence.manip = CoerceToAlignment,RemoveStops,KeepComplete(maxGapAllowed=30%),Translate(code=StandardGeneticCode) bppsuite-2.4.1/Examples/SequenceSimulation/000077500000000000000000000000001333524216000207435ustar00rootroot00000000000000bppsuite-2.4.1/Examples/SequenceSimulation/Homogeneous/000077500000000000000000000000001333524216000232335ustar00rootroot00000000000000bppsuite-2.4.1/Examples/SequenceSimulation/Homogeneous/SeqGen.bpp000066400000000000000000000026021333524216000251200ustar00rootroot00000000000000# The alphabet to use: # DNA, RNA or Protein alphabet = DNA # Input tree to use: input.tree.file = ../../Data/LSUrooted.dnd input.tree.format=Newick # Print a tree with ids as bootstrap values. # This is helpful when setting up complexe non-homogeneous models. # Setting this option will cause the program to exit after printing the tree. //output.tree.path = LSUrooted_wid.dnd # Number of sites to simulate: number_of_sites = 300 # The output file: output.sequence.file = LSUSim.fasta # The alignment format: # Must be one of Mase, Fasta, Phylip output.sequence.format = Fasta() # ---------------------------------------------------------------------------------------- # Model specification # ---------------------------------------------------------------------------------------- # Homogeneous model? # no => Homogeneous case # general => Specify the model by hand. nonhomogeneous = no # Options for homogeneous and one-per_branch models: # Available models. # For proteins, the DCmutt method is used for JTT92 and DSO78. # You can use the 'empirical' option to specify another model. # JCnuc, K80, T92, HKY85, F84, TN93, JCprot, DSO78, JTT92 or empirical # Append +G2001 or +TS98 to the model name to add a covarion model. model = HKY85(kappa=2.843, theta=0.7, theta1=0.4, theta2=0.6) # Rate Across Sites variation rate_distribution = Gamma(n=4, alpha=0.358) bppsuite-2.4.1/Examples/SequenceSimulation/HomogeneousCovarion/000077500000000000000000000000001333524216000247345ustar00rootroot00000000000000bppsuite-2.4.1/Examples/SequenceSimulation/HomogeneousCovarion/SeqGen.bpp000066400000000000000000000025471333524216000266310ustar00rootroot00000000000000# The alphabet to use: # DNA, RNA or Protein alphabet = DNA # Input tree to use: input.tree.file = ../../Data/LSUrooted.dnd input.tree.format=Newick # Print a tree with ids as bootstrap values. # This is helpful when setting up complexe non-homogeneous models. # Setting this option will cause the program to exit after printing the tree. //output.tree.path = LSUrooted_wid.dnd # Number of sites to simulate: number_of_sites = 300 # The output file: output.sequence.file = LSUSim.fasta # The alignment format: # Must be one of Mase, Fasta, Phylip output.sequence.format = Fasta() # ---------------------------------------------------------------------------------------- # Model specification # ---------------------------------------------------------------------------------------- # Homogeneous model? # no => Homogeneous case # general => Specify the model by hand. nonhomogeneous = no # Options for homogeneous and one-per_branch models: # Available models. # For proteins, the DCmutt method is used for JTT92 and DSO78. # You can use the 'empirical' option to specify another model. # JCnuc, K80, T92, HKY85, F84, TN93, JCprot, DSO78, JTT92 or empirical # Append +G2001 or +TS98 to the model name to add a covarion model. model = G01(model=HKY85(kappa=2.843, theta=0.7, theta1=0.4, theta2=0.6), rdist=Gamma(n=4, alpha=0.358), nu=1) bppsuite-2.4.1/Examples/SequenceSimulation/NonHomogeneous/000077500000000000000000000000001333524216000237065ustar00rootroot00000000000000bppsuite-2.4.1/Examples/SequenceSimulation/NonHomogeneous/SeqGen.bpp000066400000000000000000000034211333524216000255730ustar00rootroot00000000000000# The alphabet to use: # DNA, RNA or Protein alphabet = DNA # Input tree to use: input.tree.file = ../../Data/LSUrooted.dnd input.tree.format=Newick # Print a tree with ids as bootstrap values. # This is helpful when setting up complexe non-homogeneous models. # Setting this option will cause the program to exit after printing the tree. //output.tree.path = LSUrooted_wid.dnd # Number of sites to simulate: number_of_sites = 300 # The output file: output.sequence.file = LSUSim.fasta # The alignment format: # Must be one of Mase, Fasta, Phylip output.sequence.format = Fasta() # ---------------------------------------------------------------------------------------- # Model specification # ---------------------------------------------------------------------------------------- # Homogeneous model? # no => Homogeneous case # general => Specify the model by hand. nonhomogeneous = general # How to deal with root frequencies: # balanced : all frequencies are set to 1/size of the alphabet # observed : use observed counts in the data set # init : manually set the frequencies (they have to sum to one) # For nucleotides, one can use the GC rate (theta) parametrization, like in the T92 model: # balancedGC: ancestral GC set to 0.5 # observedGC: use observed GC content # initGC : manually set the ancestral GC content. nonhomogeneous.root_freq = GC(theta=0.9) # Now the general heterogeneous case: # Specify the number of distincts models. nonhomogeneous.number_of_models = 2 # Set up each model: model1=T92(kappa=2, theta=0.1) model1.nodes_id=0:62 # The Ids of the nodes to which this model should be assigned. model2=T92(kappa=1, theta=0.9) model2.nodes_id=63:155 #etc # Rate Across Sites variation rate_distribution = Gamma(n=4, alpha=0.358) bppsuite-2.4.1/Examples/SequenceSimulation/WithSiteSpecificSettings/000077500000000000000000000000001333524216000256725ustar00rootroot00000000000000bppsuite-2.4.1/Examples/SequenceSimulation/WithSiteSpecificSettings/SeqGen.bpp000066400000000000000000000030251333524216000275570ustar00rootroot00000000000000# The alphabet to use: # DNA, RNA or Protein alphabet = DNA # Input tree to use: input.tree.file = ../../Data/LSUrooted.dnd input.tree.format=Newick # Print a tree with ids as bootstrap values. # This is helpful when setting up complexe non-homogeneous models. # Setting this option will cause the program to exit after printing the tree. //output.tree.path = LSUrooted_wid.dnd #Info file specifying rate and/or ancestral state for each site: input.infos = infos.csv input.infos.rates = Rates //or 'none' to ignore rates input.infos.states = States //or 'none' to ignore states # The output file: output.sequence.file = LSUSim.fasta # The alignment format: # Must be one of Mase, Fasta, Phylip output.sequence.format = Fasta() # ---------------------------------------------------------------------------------------- # Model specification # ---------------------------------------------------------------------------------------- # Homogeneous model? # no => Homogeneous case # general => Specify the model by hand. nonhomogeneous = no # Options for homogeneous and one-per_branch models: # Available models. # For proteins, the DCmutt method is used for JTT92 and DSO78. # You can use the 'empirical' option to specify another model. # JCnuc, K80, T92, HKY85, F84, TN93, JCprot, DSO78, JTT92 or empirical # Append +G2001 or +TS98 to the model name to add a covarion model. model = HKY85(kappa=2.843, theta=0.7, theta1=0.4, theta2=0.6) # Rate Across Sites variation rate_distribution = Gamma(n=4, alpha=0.358) bppsuite-2.4.1/Examples/SequenceSimulation/WithSiteSpecificSettings/infos.csv000066400000000000000000000003201333524216000275200ustar00rootroot00000000000000Rates States 1 A 1 A 1 A 1 A 1 A 0.1 A 0.1 A 0.1 A 0.1 A 0.1 A 0.01 A 0.01 A 0.01 A 0.01 A 0.01 A 0.001 A 0.001 A 0.001 A 0.001 A 0.001 A 0.0001 A 0.0001 A 0.0001 A 0.0001 A 0.0001 A 0. A 0. A 0. A 0. A 0. A bppsuite-2.4.1/Examples/tree.dnd000066400000000000000000000023541333524216000165600ustar00rootroot00000000000000(((((((HYRAXxxxxx:0.315535,(SIRENIANxx:0.169826,ELEPHANTxx:0.267975):0.017796):0.050578,(((TENRECIDxx:0.47299,GOLDENMOLE:0.257505):0.027327,(SHEARELESH:0.202822,LOEARELESH:0.172727):0.242647):0.008795,AARDVARKxx:0.271672):0.016041):0.082056,((SLOTHxxxxx:0.205728,ANTEATERxx:0.242188):0.038477,ARMADILLOx:0.224183):0.091261):0.008608,((((SHREWxxxxx:0.339617,HEDGEHOGxx:0.561674):0.03162,MOLExxxxxx:0.264116):0.035435,((((PHYLLOSTOM:0.32093,FLYINGFOXx:0.199321):0.05832,(PANGOLINxx:0.325569,(DOGxxxxxxx:0.207802,CATxxxxxxx:0.155812):0.06783):0.014326):0.005336,((TAPIRxxxxx:0.121045,RHINOxxxxx:0.106818):0.018155,HORSExxxxx:0.133168):0.07215):0.00621,((PIGxxxxxxx:0.21458,(COWxxxxxxx:0.210751,((WHALExxxxx:0.069143,DELPHINOID:0.106709):0.08502,HIPPOxxxxx:0.15055):0.024995):0.027182):0.015181,LLAMAxxxxx:0.220994):0.066573):0.014501):0.039814,(((FLYINGLEMU:0.282117,(HUMANxxxxx:0.308645,STREPSIRRH:0.261181):0.030928):0.014734,((RABBITxxxx:0.201429,PIKAxxxxxx:0.309796):0.116321,(SCIURIDxxx:0.297008,((RATxxxxxxx:0.152806,MOUSExxxxx:0.151811):0.365769,CAVIOMORPH:0.446645):0.020092):0.036422):0.015393):0.006639,TREESHREWx:0.340069):0.023397):0.018412):0.353693,PLATYPUSxx:0.654498):0.417347,DIPROTODON:0.196688):0.14091,MONODELPHI:0.16331,DIDELPHISx:0.161116); bppsuite-2.4.1/INSTALL.txt000066400000000000000000000015751333524216000152270ustar00rootroot00000000000000This software needs cmake >= 2.8.11 and a C++11 capable compiler to build After installing cmake, run it with the following command: $ cmake -DCMAKE_INSTALL_PREFIX=[where to install, for instance /usr/local or $HOME/.local] . If available, you can also use ccmake instead of cmake for a more user-friendly interface. Then compile and install the software with: $ make install You may also consider installing and using the software checkinstall for easier system administration. If you install Bio++ in a non standard path (not /usr/), and compile bppsuite with shared libraries, you must also tell programs where to find them at startup: -> either by adding the path to LD_LIBRARY_PATH environment variable. -> or by using RPATHs to hard code the path in the executable (generates NON PORTABLE executables !) -> install Bio++ with the "-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE" option bppsuite-2.4.1/NEWS000066400000000000000000000000001333524216000140350ustar00rootroot00000000000000bppsuite-2.4.1/README.md000066400000000000000000000042451333524216000146340ustar00rootroot00000000000000# BppSuite presentation BppSuite is a suite of ready-to-use programs for phylogenetic and sequence analysis. ## Installation ### Standalone executables Standalone executables are available for [linux64](https://github.com/BioPP/bppsuite/releases/tag/v2.3.2) [//]: [win32](http://biopp.univ-montp2.fr/repos/exe/win32/), [win64](http://biopp.univ-montp2.fr/repos/exe/win64/) and [Mac](http://biopp.univ-montp2.fr/repos/exe/mac/) ### From source files #### Get the sources This is done with git, for example in directory $bpp_dir:
cd $bpp_dir
git clone https://github.com/BioPP/bppsuite
#### Compiling Bio++ libraries need to be installed beforehand, for example in $bpp_dir. The needed libraries are [bpp-core](https://github.com/BioPP/bpp-core), [bpp-seq](https://github.com/BioPP/bpp-seq), [bpp-phyl](https://github.com/BioPP/bpp-phyl), [bpp-popgen](https://github.com/BioPP/bpp-popgen). After, you proceed:
cd bppsuite
cmake -DCMAKE_INSTALL_PREFIX=$bpp_dir ./ # prepare compilation
make # compile
make install # move files to the installation directory (this will create a $bpp_dir/bin/ directory)
That's it ! The executables are now installed in $bpp_dir/bin. Without the option -DCMAKE_INSTALL_PREFIX=$bpp_dir, the standard /usr/local directory will be used, and the executables installed in /usr/local/bin, a location which requires superuser access rights. ## Usage Bppsuite executables should know where the dynamic libraries are. A way to check it is the command:
ldd $bpp_dir$/bin/bppml
To configure this, set in the shell environment variable :
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$bpp_dir
(and source the configuration file or relog). ## Documentation You can also generate the pdf documentation by typing :
make pdf
### Examples Many examples are available in the subdirectory of Examples. ### Documentation Documentation can be found in one page at: http://bioweb.me/bppsuite-doc Or on github: https://github.com/BioPP/bppsuite/releases/tag/v2.3.2 in pdf or html. bppsuite-2.4.1/bppSuite/000077500000000000000000000000001333524216000151435ustar00rootroot00000000000000bppsuite-2.4.1/bppSuite/CMakeLists.txt000066400000000000000000000026521333524216000177100ustar00rootroot00000000000000# CMake script for Bio++ Program Suite # Authors: # Julien Dutheil # Francois Gindraud (2017) # Created: 22/08/2009 # Executables of bppsuite. # Generation of targets from file name is not automated in case of executables not following the pattern. add_executable (bppml bppML.cpp) add_executable (bppseqgen bppSeqGen.cpp) add_executable (bppdist bppDist.cpp) add_executable (bpppars bppPars.cpp) add_executable (bppseqman bppSeqMan.cpp) add_executable (bppconsense bppConsense.cpp) add_executable (bppancestor bppAncestor.cpp) add_executable (bppmixedlikelihoods bppMixedLikelihoods.cpp) add_executable (bppreroot bppReRoot.cpp) add_executable (bpptreedraw bppTreeDraw.cpp) add_executable (bppalnscore bppAlnScore.cpp) add_executable (bpppopstats bppPopStats.cpp) set (bppsuite-targets bppml bppseqgen bppdist bpppars bppseqman bppconsense bppancestor bppmixedlikelihoods bppreroot bpptreedraw bppalnscore bpppopstats ) foreach (target ${bppsuite-targets}) # Link (static or shared) if (BUILD_STATIC) target_link_libraries (${target} ${BPP_LIBS_STATIC}) set_target_properties (${target} PROPERTIES LINK_SEARCH_END_STATIC TRUE) else (BUILD_STATIC) target_link_libraries (${target} ${BPP_LIBS_SHARED}) set_target_properties (${target} PROPERTIES POSITION_INDEPENDENT_CODE TRUE) endif (BUILD_STATIC) endforeach (target) install (TARGETS ${bppsuite-targets} DESTINATION ${CMAKE_INSTALL_BINDIR}) bppsuite-2.4.1/bppSuite/bppAlnScore.cpp000066400000000000000000000233641333524216000200670ustar00rootroot00000000000000// // File: bppAlnScore.cpp // Created by: Julien Dutheil // Created on: Dec Thu 15 16:16 2011 // /* Copyright or © or Copr. Bio++ Development Team This software is a computer program whose purpose is to simulate sequence data according to a phylogenetic tree and an evolutionary model. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. */ // From the STL: #include #include #include using namespace std; #include #include #include #include #include // From bpp-seq: #include #include #include #include #include #include using namespace bpp; void help() { (*ApplicationTools::message << "__________________________________________________________________________").endLine(); (*ApplicationTools::message << "bppalnscore parameter1_name=parameter1_value").endLine(); (*ApplicationTools::message << " parameter2_name=parameter2_value ... param=option_file").endLine(); (*ApplicationTools::message).endLine(); (*ApplicationTools::message << " Refer to the Bio++ Program Suite Manual for a list of available options.").endLine(); (*ApplicationTools::message << "__________________________________________________________________________").endLine(); } int main(int args, char** argv) { cout << "******************************************************************" << endl; cout << "* Bio++ Alignment Score, version " << BPP_VERSION << " *" << endl; cout << "* Author: J. Dutheil Last Modif. " << BPP_REL_DATE << " *" << endl; cout << "******************************************************************" << endl; cout << endl; if (args == 1) { help(); return 0; } try { BppApplication bppalnscore(args, argv, "BppAlnScore"); bppalnscore.startTimer(); // Get alphabet Alphabet* alphabet = SequenceApplicationTools::getAlphabet(bppalnscore.getParams(), "", false, true, true); // Get the test alignment: unique_ptr sitesTest(SequenceApplicationTools::getSiteContainer(alphabet, bppalnscore.getParams(), ".test", false, true)); // Get the reference alignment: unique_ptr sitesRef(SequenceApplicationTools::getSiteContainer(alphabet, bppalnscore.getParams(), ".ref", false, true)); // We check if the two alignments are compatible: vector namesTest = sitesTest->getSequencesNames(); vector namesRef = sitesRef->getSequencesNames(); if (namesTest != namesRef) { ApplicationTools::displayTask("Reorder sequences in ref. alignment", true); unique_ptr tmp(new AlignedSequenceContainer(sitesRef->getAlphabet())); for (size_t i = 0; i < namesTest.size(); ++i) { ApplicationTools::displayGauge(i, namesTest.size() - 1); try { tmp->addSequence(sitesRef->getSequence(namesTest[i])); } catch (SequenceNotFoundException& ex) { throw Exception("ERROR!!! Reference alignment should contain the same sequences as the test alignment!"); } } ApplicationTools::displayTaskDone(); sitesRef = move(tmp); } // Build alignment indexes: RowMatrix indexTest, indexRef; SiteContainerTools::getSequencePositions(*sitesTest, indexTest); SiteContainerTools::getSequencePositions(*sitesRef, indexRef); // Now build scores: int na = ApplicationTools::getIntParameter("score.na", bppalnscore.getParams(), 0); ApplicationTools::displayResult("NA value to used", na); vector cs = SiteContainerTools::getColumnScores(indexTest, indexRef, na); vector sps = SiteContainerTools::getSumOfPairsScores(indexTest, indexRef, static_cast(na)); // Should scores be averaged for words? size_t wsize = ApplicationTools::getParameter("score.word_size", bppalnscore.getParams(), 1); size_t phase = 0; if (wsize > 1) { ApplicationTools::displayResult("Scores uniformized for words of size", wsize); string phaseOpt = ApplicationTools::getStringParameter("score.phase", bppalnscore.getParams(), "1"); if (TextTools::isDecimalInteger(phaseOpt)) { phase = TextTools::to(phaseOpt); if (phase == 0) throw Exception("ERROR: positions are 1-based."); phase--; } else { // We look for the first occurrence of the given motif: try { BasicSequence motif("motif", phaseOpt, sitesTest->getAlphabet()); ApplicationTools::displayResult("Phase based on 1st occurence of", motif.toString()); size_t pos = sitesTest->getNumberOfSites(); for (size_t i = 0; i < sitesTest->getNumberOfSequences(); ++i) { size_t p = SequenceTools::findFirstOf(sitesTest->getSequence(i), motif); if (p < pos) pos = p; } phase = pos; } catch (Exception& ex) { throw Exception("Error, unvalid motif specified for phase option."); } } ApplicationTools::displayResult("First word starts at", phase + 1); // Now perform the smoothing: size_t i; for (i = 0; i < phase; ++i) { cs[i] = 0; sps[i] = 0; } for ( ; i + wsize <= cs.size(); i += wsize) { // First compute minimum criterion: int csmin = 1; double spsmin = 1; for (size_t j = i; j < i + wsize; ++j) { if (cs[j] < csmin) csmin = cs[j]; if (sps[j] < spsmin) spsmin = sps[j]; } // Assign min to all positions in word: for (size_t j = i; j < i + wsize; ++j) { cs[j] = csmin; sps[j] = spsmin; } } for ( ; i < cs.size(); ++i) { cs[i] = 0; sps[i] = 0; } } // Output scores to file: string outputScores = ApplicationTools::getAFilePath("output.scores", bppalnscore.getParams(), false, false); if (outputScores != "none") { ApplicationTools::displayResult("Output scores to", outputScores); ofstream output(outputScores.c_str(), ios::out); output << "Site\tColumnScore\tSumOfPairsScore" << endl; for (size_t i = 0; i < cs.size(); ++i) { output << sitesTest->getSite(i).getPosition() << "\t" << cs[i] << "\t" << sps[i] << endl; } output.close(); } // Create a sequence filter: string outputFilter = ApplicationTools::getAFilePath("output.mase", bppalnscore.getParams(), false, false); if (outputFilter != "none") { ApplicationTools::displayResult("Output mase with site filter to", outputFilter); double spsThreshold = ApplicationTools::getDoubleParameter("output.sps_thresholds", bppalnscore.getParams(), 0.8); ApplicationTools::displayResult("Threshold for SPS", spsThreshold); MultiRange csRanges; MultiRange spsRanges; size_t csBeg = 0, spsBeg = 0, csEnd = 0, spsEnd = 0; size_t s = alphabet->getStateCodingSize(); for (size_t i = 0; i < cs.size(); ++i) { if (cs[i] == 1 && i > 0 && cs[i-1] != 1) csBeg = i; if (cs[i] != 1 && i > 0 && cs[i-1] == 1) { csEnd = i; csRanges.addRange(Range(csBeg * s, csEnd * s)); } if (sps[i] >= spsThreshold && i > 0 && sps[i-1] < spsThreshold) spsBeg = i; if (sps[i] < spsThreshold && i > 0 && sps[i-1] >= spsThreshold) { spsEnd = i; spsRanges.addRange(Range(spsBeg * s, spsEnd * s)); } } //Add the last range if any: if (cs.back() == 1) csRanges.addRange(Range(csBeg * s, cs.size() * s)); if (sps.back() >= spsThreshold) spsRanges.addRange(Range(spsBeg * s, sps.size() * s)); MaseHeader header; header.setSiteSelection("CS", csRanges); header.setSiteSelection("SPS", spsRanges); Mase writer; writer.writeMeta(outputFilter, *sitesTest, header); } // We're done! bppalnscore.done(); } catch (exception& e) { cout << e.what() << endl; return 1; } return 0; } bppsuite-2.4.1/bppSuite/bppAncestor.cpp000066400000000000000000000511451333524216000201350ustar00rootroot00000000000000// // File: bppAncestor.cpp // Created by: Julien Dutheil // Created on: Sep Wed 10 14:14 2008 // /* Copyright or © or Copr. Bio++ Development Team This software is a computer program whose purpose is to estimate phylogenies and evolutionary parameters from a dataset according to the maximum likelihood principle. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. */ // From the STL: #include #include using namespace std; // From bpp-core: #include #include #include #include #include #include #include #include #include #include #include // From bpp-seq: #include #include #include #include #include #include // From bpp-phyl: #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include using namespace bpp; /******************************************************************************/ void help() { (*ApplicationTools::message << "__________________________________________________________________________").endLine(); (*ApplicationTools::message << "bppancestor parameter1_name=parameter1_value ").endLine(); (*ApplicationTools::message << " parameter2_name=parameter2_value ... param=option_file").endLine(); (*ApplicationTools::message).endLine(); (*ApplicationTools::message << " Refer to the Bio++ Program Suite Manual for a list of available options.").endLine(); (*ApplicationTools::message << "__________________________________________________________________________").endLine(); } int main(int args, char ** argv) { cout << "******************************************************************" << endl; cout << "* Bio++ Ancestral Sequence Reconstruction, version " << BPP_VERSION << " *" << endl; cout << "* Authors: J. Dutheil Created on: 10/09/08 *" << endl; cout << "* B. Boussau Last Modif: " << BPP_REL_DATE << " *" << endl; cout << "******************************************************************" << endl; cout << endl; if (args == 1) { help(); return 0; } try { BppApplication bppancestor(args, argv, "BppAncestor"); bppancestor.startTimer(); Alphabet* alphabet = SequenceApplicationTools::getAlphabet(bppancestor.getParams(), "", false); unique_ptr gCode; CodonAlphabet* codonAlphabet = dynamic_cast(alphabet); if (codonAlphabet) { string codeDesc = ApplicationTools::getStringParameter("genetic_code", bppancestor.getParams(), "Standard", "", true, true); ApplicationTools::displayResult("Genetic Code", codeDesc); gCode.reset(SequenceApplicationTools::getGeneticCode(codonAlphabet->getNucleicAlphabet(), codeDesc)); } VectorSiteContainer* allSites = SequenceApplicationTools::getSiteContainer(alphabet, bppancestor.getParams()); VectorSiteContainer* sites = SequenceApplicationTools::getSitesToAnalyse(* allSites, bppancestor.getParams(), "", true, false); delete allSites; ApplicationTools::displayResult("Number of sequences", TextTools::toString(sites->getNumberOfSequences())); ApplicationTools::displayResult("Number of sites", TextTools::toString(sites->getNumberOfSites())); // Get the initial tree Tree* tree = PhylogeneticsApplicationTools::getTree(bppancestor.getParams()); ApplicationTools::displayResult("Number of leaves", TextTools::toString(tree->getNumberOfLeaves())); string treeWIdPath = ApplicationTools::getAFilePath("output.tree_ids.file", bppancestor.getParams(), false, false); if (treeWIdPath != "none") { TreeTemplate ttree(*tree); vector nodes = ttree.getNodes(); for(unsigned int i = 0; i < nodes.size(); i++) { if(nodes[i]->isLeaf()) nodes[i]->setName(TextTools::toString(nodes[i]->getId()) + "_" + nodes[i]->getName()); else nodes[i]->setBranchProperty("NodeId", BppString(TextTools::toString(nodes[i]->getId()))); } Newick treeWriter; treeWriter.enableExtendedBootstrapProperty("NodeId"); ApplicationTools::displayResult("Writing tagged tree to", treeWIdPath); treeWriter.write(ttree, treeWIdPath); delete tree; cout << "BppAncestor's done." << endl; exit(0); } bool checkTree = ApplicationTools::getBooleanParameter("input.tree.check_root", bppancestor.getParams(), true, "", true, false); DRTreeLikelihood *tl; string nhOpt = ApplicationTools::getStringParameter("nonhomogeneous", bppancestor.getParams(), "no", "", true, false); ApplicationTools::displayResult("Heterogeneous model", nhOpt); TransitionModel *model = 0; SubstitutionModelSet *modelSet = 0; DiscreteDistribution *rDist = 0; size_t nbStates; if (nhOpt == "no") { model = PhylogeneticsApplicationTools::getTransitionModel(alphabet, gCode.get(), sites, bppancestor.getParams()); if (model->getName() != "RE08") SiteContainerTools::changeGapsToUnknownCharacters(*sites); if (model->getNumberOfStates() > model->getAlphabet()->getSize()) { //Markov-modulated Markov model! rDist = new ConstantRateDistribution(); } else { rDist = PhylogeneticsApplicationTools::getRateDistribution(bppancestor.getParams()); } if (dynamic_cast(model)) tl = new DRHomogeneousMixedTreeLikelihood(*tree, *sites, model, rDist, checkTree, true, true); else tl = new DRHomogeneousTreeLikelihood(*tree, *sites, model, rDist, checkTree); nbStates = model->getNumberOfStates(); } else if (nhOpt == "one_per_branch") { model = PhylogeneticsApplicationTools::getTransitionModel(alphabet, gCode.get(), sites, bppancestor.getParams()); if (model->getName() != "RE08") SiteContainerTools::changeGapsToUnknownCharacters(*sites); if (model->getNumberOfStates() > model->getAlphabet()->getSize()) { //Markov-modulated Markov model! rDist = new ConstantRateDistribution(); } else { rDist = PhylogeneticsApplicationTools::getRateDistribution(bppancestor.getParams()); } vector rateFreqs; if (model->getNumberOfStates() != alphabet->getSize()) { //Markov-Modulated Markov Model... unsigned int n =(unsigned int)(model->getNumberOfStates() / alphabet->getSize()); rateFreqs = vector(n, 1./(double)n); // Equal rates assumed for now, may be changed later (actually, in the most general case, // we should assume a rate distribution for the root also!!! } std::map aliasFreqNames; FrequenciesSet * rootFreqs = PhylogeneticsApplicationTools::getRootFrequenciesSet(alphabet, gCode.get(), sites, bppancestor.getParams(), aliasFreqNames, rateFreqs); vector globalParameters = ApplicationTools::getVectorParameter("nonhomogeneous_one_per_branch.shared_parameters", bppancestor.getParams(), ',', ""); modelSet = SubstitutionModelSetTools::createNonHomogeneousModelSet(model, rootFreqs, tree, aliasFreqNames, globalParameters); model = 0; if (dynamic_cast(modelSet)) throw Exception("Non-homogeneous mixed substitution ancestor reconstruction not implemented, sorry!"); tl = new DRNonHomogeneousTreeLikelihood(*tree, *sites, modelSet, rDist, true); nbStates = modelSet->getNumberOfStates(); } else if (nhOpt == "general") { modelSet = PhylogeneticsApplicationTools::getSubstitutionModelSet(alphabet, gCode.get(), sites, bppancestor.getParams()); if (modelSet->getModel(0)->getName() != "RE08") SiteContainerTools::changeGapsToUnknownCharacters(*sites); if (modelSet->getNumberOfStates() > modelSet->getAlphabet()->getSize()) { //Markov-modulated Markov model! rDist = new ConstantDistribution(1.); } else { rDist = PhylogeneticsApplicationTools::getRateDistribution(bppancestor.getParams()); } if (dynamic_cast(modelSet)) throw Exception("Non-homogeneous mixed substitution ancestor reconstruction not implemented, sorry!"); tl = new DRNonHomogeneousTreeLikelihood(*tree, *sites, modelSet, rDist, true); nbStates = modelSet->getNumberOfStates(); } else throw Exception("Unknown option for nonhomogeneous: " + nhOpt); tl->initialize(); delete tree; double logL = tl->getValue(); if (std::isinf(logL)) { // This may be due to null branch lengths, leading to null likelihood! ApplicationTools::displayWarning("!!! Warning!!! Likelihood is zero."); ApplicationTools::displayWarning("!!! This may be due to branch length == 0."); ApplicationTools::displayWarning("!!! All null branch lengths will be set to 0.000001."); ParameterList pl = tl->getBranchLengthsParameters(); for(unsigned int i = 0; i < pl.size(); i++) { if(pl[i].getValue() < 0.000001) pl[i].setValue(0.000001); } tl->matchParametersValues(pl); logL = tl->getValue(); } if (std::isinf(logL)) { ApplicationTools::displayError("!!! Unexpected likelihood == 0."); ApplicationTools::displayError("!!! Looking at each site:"); for(unsigned int i = 0; i < sites->getNumberOfSites(); i++) { (*ApplicationTools::error << "Site " << sites->getSite(i).getPosition() << "\tlog likelihood = " << tl->getLogLikelihoodForASite(i)).endLine(); } ApplicationTools::displayError("!!! 0 values (inf in log) may be due to computer overflow, particularily if datasets are big (>~500 sequences)."); exit(-1); } tree = new TreeTemplate(tl->getTree()); // Write parameters to screen: ApplicationTools::displayResult("Log likelihood", TextTools::toString(tl->getValue(), 15)); ParameterList parameters = tl->getSubstitutionModelParameters(); for (unsigned int i = 0; i < parameters.size(); i++) { ApplicationTools::displayResult(parameters[i].getName(), TextTools::toString(parameters[i].getValue())); } parameters = tl->getRateDistributionParameters(); for (unsigned int i = 0; i < parameters.size(); i++) { ApplicationTools::displayResult(parameters[i].getName(), TextTools::toString(parameters[i].getValue())); } // Getting posterior rate class distribution: DiscreteDistribution* prDist = RASTools::getPosteriorRateDistribution(*tl); ApplicationTools::displayMessage("\nPosterior rate distribution for dataset:\n"); if (ApplicationTools::message) prDist->print(*ApplicationTools::message); ApplicationTools::displayMessage("\n"); delete prDist; // Reconstruct ancestral sequences: string reconstruction = ApplicationTools::getStringParameter("asr.method", bppancestor.getParams(), "marginal", "", true, false); ApplicationTools::displayResult("Ancestral state reconstruction method", reconstruction); bool probs = false; AncestralStateReconstruction *asr = 0; bool probMethod = false; if (reconstruction == "none") { //do nothing } else if (reconstruction == "marginal") { asr = new MarginalAncestralStateReconstruction(tl); probMethod = true; } else throw Exception("Unknown ancestral state reconstruction method: " + reconstruction); string outputFile; if (asr) { if (probMethod) { probs = ApplicationTools::getBooleanParameter("asr.probabilities", bppancestor.getParams(), false, "", true, false); ApplicationTools::displayResult("Output probabilities", probs ? "yes" : "no"); } // Write infos to file: outputFile = ApplicationTools::getAFilePath("output.sites.file", bppancestor.getParams(), false, false); if (outputFile != "none") { ApplicationTools::displayResult("Output file for sites", outputFile); ofstream out(outputFile.c_str(), ios::out); TreeTemplate ttree(*tree); vector nodes = ttree.getInnerNodes(); size_t nbNodes = nodes.size(); // Get the rate class with maximum posterior probability: vector classes = tl->getRateClassWithMaxPostProbOfEachSite(); // Get the posterior rate, i.e. rate averaged over all posterior probabilities: Vdouble rates = tl->getPosteriorRateOfEachSite(); // Get the ancestral sequences: vector sequences(nbNodes); vector probabilities(nbNodes); vector colNames; colNames.push_back("Sites"); colNames.push_back("is.complete"); colNames.push_back("is.constant"); colNames.push_back("lnL"); colNames.push_back("rc"); colNames.push_back("pr"); for (size_t i = 0; i < nbNodes; i++) { Node *node = nodes[i]; colNames.push_back("max." + TextTools::toString(node->getId())); if (probs) { probabilities[i] = new VVdouble(); //The cast will have to be updated when more probabilistic method will be available: sequences[i] = dynamic_cast(asr)->getAncestralSequenceForNode(node->getId(), probabilities[i], false); for (unsigned int j = 0; j < nbStates; j++) { colNames.push_back("prob." + TextTools::toString(node->getId()) + "." + alphabet->intToChar((int)j)); } } else { if (node->isLeaf()) { } else { sequences[i] = asr->getAncestralSequenceForNode(node->getId()); } } } //Now fill the table: vector row(colNames.size()); DataTable* infos = new DataTable(colNames); for (size_t i = 0; i < sites->getNumberOfSites(); i++) { double lnL = tl->getLogLikelihoodForASite(i); const Site* currentSite = &sites->getSite(i); int currentSitePosition = currentSite->getPosition(); string isCompl = "NA"; string isConst = "NA"; try { isCompl = (SiteTools::isComplete(*currentSite) ? "1" : "0"); } catch(EmptySiteException& ex) {} try { isConst = (SiteTools::isConstant(*currentSite) ? "1" : "0"); } catch(EmptySiteException& ex) {} row[0] = (string("[" + TextTools::toString(currentSitePosition) + "]")); row[1] = isCompl; row[2] = isConst; row[3] = TextTools::toString(lnL); row[4] = TextTools::toString(classes[i]); row[5] = TextTools::toString(rates[i]); size_t k = 6; for (size_t j = 0; j < nbNodes; j++) { row[k] = sequences[j]->getChar(i); k++; if (probs) { for (size_t l = 0; l < nbStates; l++) { row[k] = TextTools::toString((*probabilities[j])[i][l]); k++; } } } infos->addRow(row); } DataTable::write(*infos, out, "\t"); delete infos; } SiteContainer* asSites = 0; if (probMethod) { bool sample = ApplicationTools::getBooleanParameter("asr.sample", bppancestor.getParams(), false, "", true, false); ApplicationTools::displayResult("Sample from posterior distribution", sample ? "yes" : "no"); if (sample) { unsigned int nbSamples = ApplicationTools::getParameter("asr.sample.number", bppancestor.getParams(), 1, "", true, false); asSites = new AlignedSequenceContainer(alphabet); for (unsigned int i = 0; i < nbSamples; i++) { ApplicationTools::displayGauge(i, nbSamples-1, '='); SequenceContainer *sampleSites = dynamic_cast(asr)->getAncestralSequences(true); vector names = sampleSites->getSequencesNames(); for (unsigned int j = 0; j < names.size(); j++) names[j] += "_" + TextTools::toString(i+1); sampleSites->setSequencesNames(names, false); SequenceContainerTools::append(*asSites, *sampleSites); delete sampleSites; } ApplicationTools::message->endLine(); } else { asSites = asr->getAncestralSequences(); } } else { asSites = asr->getAncestralSequences(); } //Add existing sequence to output? bool addExtant = ApplicationTools::getBooleanParameter("asr.add_extant", bppancestor.getParams(), false, "", true, false); if (addExtant) { SequenceContainerTools::append(*asSites, *sites); } //Write output: if (ApplicationTools::getStringParameter("output.sequence.file", bppancestor.getParams(), "none") != "none") { SequenceApplicationTools::writeAlignmentFile(*asSites, bppancestor.getParams()); } delete asSites; delete asr; } outputFile = ApplicationTools::getAFilePath("output.nodes.file", bppancestor.getParams(), false, false); if (outputFile != "none") { ApplicationTools::displayResult("Output file for nodes", outputFile); ofstream out(outputFile.c_str(), ios::out); //Add existing sequence to output? bool addExtant = ApplicationTools::getBooleanParameter("output.nodes.add_extant", bppancestor.getParams(), false, "", true, false); map > frequencies; TreeLikelihoodTools::getAncestralFrequencies(*tl, frequencies, addExtant); vector colNames; colNames.push_back("Nodes"); for (unsigned int i = 0; i < tl->getNumberOfStates(); i++) colNames.push_back("exp" + tl->getAlphabetStateAsChar(i)); for (unsigned int i = 0; i < tl->getNumberOfStates(); i++) colNames.push_back("eb" + tl->getAlphabetStateAsChar(i)); //Now fill the table: vector row(colNames.size()); DataTable* infos = new DataTable(colNames); for (map >::iterator it = frequencies.begin(); it != frequencies.end(); it++) { row[0] = TextTools::toString(it->first); Vdouble ebFreqs = DRTreeLikelihoodTools::getPosteriorStateFrequencies(*tl, it->first); for (unsigned int i = 0; i < tl->getNumberOfStates(); i++) { row[i + 1] = TextTools::toString(it->second[i]); } for (unsigned int i = 0; i < tl->getNumberOfStates(); i++) { row[i + tl->getNumberOfStates() + 1] = TextTools::toString(ebFreqs[i]); } infos->addRow(row); } DataTable::write(*infos, out, "\t"); delete infos; } delete alphabet; delete sites; if(model) delete model; if(modelSet) delete modelSet; delete rDist; delete tl; delete tree; bppancestor.done(); } catch (exception & e) { cout << e.what() << endl; return 1; } return 0; } bppsuite-2.4.1/bppSuite/bppConsense.cpp000066400000000000000000000116621333524216000201340ustar00rootroot00000000000000// // File: bppConsense.cpp // Created by: Julien Dutheil // Created on: Jun Wed 06 11:17 2007 // /* Copyright or © or Copr. CNRS This software is a computer program whose purpose is to estimate phylogenies and evolutionary parameters from a dataset according to the maximum likelihood principle. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. */ // From the STL: #include #include using namespace std; // From bpp-core: #include #include #include #include #include #include // From bpp-phyl: #include #include #include using namespace bpp; void help() { (*ApplicationTools::message << "__________________________________________________________________________").endLine(); (*ApplicationTools::message << "bppconsense parameter1_name=parameter1_value").endLine(); (*ApplicationTools::message << " parameter2_name=parameter2_value ... param=option_file").endLine(); (*ApplicationTools::message).endLine(); (*ApplicationTools::message << " Refer to the Bio++ Program Suite Manual for a list of available options.").endLine(); (*ApplicationTools::message << "__________________________________________________________________________").endLine(); } int main(int args, char ** argv) { cout << "******************************************************************" << endl; cout << "* Bio++ Consensus and Bootstrap Methods, version " << BPP_VERSION << " *" << endl; cout << "* Authors: J. Dutheil Created 06/06/07 *" << endl; cout << "* N. Galtier Last Modif. " << BPP_REL_DATE << " *" << endl; cout << "******************************************************************" << endl; cout << endl; if(args == 1) { help(); return 0; } try { BppApplication bppconsense(args, argv, "BppConsense"); bppconsense.startTimer(); vector list = PhylogeneticsApplicationTools::getTrees(bppconsense.getParams()); Tree* tree = 0; string treeMethod = ApplicationTools::getStringParameter("tree", bppconsense.getParams(), "Consensus", "", false, 1); string cmdName; map cmdArgs; KeyvalTools::parseProcedure(treeMethod, cmdName, cmdArgs); if(cmdName == "Input") { tree = PhylogeneticsApplicationTools::getTree(bppconsense.getParams()); ApplicationTools::displayResult("Number of leaves", tree->getNumberOfLeaves()); } else if(cmdName == "Consensus") { double threshold = ApplicationTools::getDoubleParameter("threshold", cmdArgs, 0, "", false, 1); ApplicationTools::displayResult("Consensus threshold", TextTools::toString(threshold)); ApplicationTools::displayTask("Computing consensus tree"); tree = TreeTools::thresholdConsensus(list, threshold, true); ApplicationTools::displayTaskDone(); } else throw Exception("Unknown input tree method: " + treeMethod); ApplicationTools::displayTask("Compute bootstrap values"); int bsformat = ApplicationTools::getIntParameter("bootstrap.format", bppconsense.getParams(), 0, "", false, 1); TreeTools::computeBootstrapValues(*tree, list, true, bsformat); ApplicationTools::displayTaskDone(); //Write resulting tree: PhylogeneticsApplicationTools::writeTree(*tree, bppconsense.getParams()); for (size_t i = 0; i < list.size(); i++) delete list[i]; delete tree; bppconsense.done(); } catch(exception & e) { cout << e.what() << endl; return 1; } return (0); } bppsuite-2.4.1/bppSuite/bppDist.cpp000066400000000000000000000352371333524216000172660ustar00rootroot00000000000000// // File: bppDist.cpp // Created by: Julien Dutheil // Created on: May Sat 05 15:09 2007 // From file bppML.cpp // /* Copyright or © or Copr. Bio++ Development Team This software is a computer program whose purpose is to estimate phylogenies and evolutionary parameters from a dataset according to the maximum likelihood principle. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. */ // From the STL: #include #include using namespace std; // From bpp-core: #include #include #include #include #include #include #include // From bpp-seq: #include #include #include #include #include #include // From bpp-phyl: #include #include #include #include #include #include #include #include #include #include #include #include using namespace bpp; void help() { (*ApplicationTools::message << "__________________________________________________________________________").endLine(); (*ApplicationTools::message << "bppdist parameter1_name=parameter1_value parameter2_name=parameter2_value").endLine(); (*ApplicationTools::message << " ... param=option_file").endLine(); (*ApplicationTools::message).endLine(); (*ApplicationTools::message << " Refer to the Bio++ Program Suite Manual for a list of available options.").endLine(); (*ApplicationTools::message << "__________________________________________________________________________").endLine(); } int main(int args, char ** argv) { cout << "******************************************************************" << endl; cout << "* Bio++ Distance Methods, version " << BPP_VERSION << " *" << endl; cout << "* Author: J. Dutheil Created 05/05/07 *" << endl; cout << "* Last Modif. " << BPP_REL_DATE << " *" << endl; cout << "******************************************************************" << endl; cout << endl; if(args == 1) { help(); return 0; } try { BppApplication bppdist(args, argv, "BppDist"); bppdist.startTimer(); Alphabet* alphabet = SequenceApplicationTools::getAlphabet(bppdist.getParams(), "", false); unique_ptr gCode; CodonAlphabet* codonAlphabet = dynamic_cast(alphabet); if (codonAlphabet) { string codeDesc = ApplicationTools::getStringParameter("genetic_code", bppdist.getParams(), "Standard", "", true, true); ApplicationTools::displayResult("Genetic Code", codeDesc); gCode.reset(SequenceApplicationTools::getGeneticCode(codonAlphabet->getNucleicAlphabet(), codeDesc)); } VectorSiteContainer* allSites = SequenceApplicationTools::getSiteContainer(alphabet, bppdist.getParams()); VectorSiteContainer* sites = SequenceApplicationTools::getSitesToAnalyse(* allSites, bppdist.getParams()); delete allSites; ApplicationTools::displayResult("Number of sequences", TextTools::toString(sites->getNumberOfSequences())); ApplicationTools::displayResult("Number of sites", TextTools::toString(sites->getNumberOfSites())); TransitionModel* model = PhylogeneticsApplicationTools::getTransitionModel(alphabet, gCode.get(), sites, bppdist.getParams()); DiscreteDistribution* rDist = 0; if (model->getNumberOfStates() > model->getAlphabet()->getSize()) { //Markov-modulated Markov model! rDist = new ConstantRateDistribution(); } else { rDist = PhylogeneticsApplicationTools::getRateDistribution(bppdist.getParams()); } DistanceEstimation distEstimation(model, rDist, sites, 1, false); string method = ApplicationTools::getStringParameter("method", bppdist.getParams(), "nj"); ApplicationTools::displayResult("Tree reconstruction method", method); TreeTemplate* tree; AgglomerativeDistanceMethod* distMethod = 0; if(method == "wpgma") { PGMA* wpgma = new PGMA(true); distMethod = wpgma; } else if(method == "upgma") { PGMA* upgma = new PGMA(false); distMethod = upgma; } else if(method == "nj") { NeighborJoining* nj = new NeighborJoining(); nj->outputPositiveLengths(true); distMethod = nj; } else if(method == "bionj") { BioNJ* bionj = new BioNJ(); bionj->outputPositiveLengths(true); distMethod = bionj; } else throw Exception("Unknown tree reconstruction method."); string type = ApplicationTools::getStringParameter("optimization.method", bppdist.getParams(), "init"); ApplicationTools::displayResult("Model parameters estimation method", type); if (type == "init") type = OptimizationTools::DISTANCEMETHOD_INIT; else if (type == "pairwise") type = OptimizationTools::DISTANCEMETHOD_PAIRWISE; else if (type == "iterations") type = OptimizationTools::DISTANCEMETHOD_ITERATIONS; else throw Exception("Unknown parameter estimation procedure '" + type + "'."); unsigned int optVerbose = ApplicationTools::getParameter("optimization.verbose", bppdist.getParams(), 2); string mhPath = ApplicationTools::getAFilePath("optimization.message_handler", bppdist.getParams(), false, false); OutputStream* messenger = (mhPath == "none") ? 0 : (mhPath == "std") ? ApplicationTools::message.get() : new StlOutputStream(new ofstream(mhPath.c_str(), ios::out)); ApplicationTools::displayResult("Message handler", mhPath); string prPath = ApplicationTools::getAFilePath("optimization.profiler", bppdist.getParams(), false, false); OutputStream* profiler = (prPath == "none") ? 0 : (prPath == "std") ? ApplicationTools::message.get() : new StlOutputStream(new ofstream(prPath.c_str(), ios::out)); if(profiler) profiler->setPrecision(20); ApplicationTools::displayResult("Profiler", prPath); // Should I ignore some parameters? ParameterList allParameters = model->getParameters(); allParameters.addParameters(rDist->getParameters()); ParameterList parametersToIgnore; string paramListDesc = ApplicationTools::getStringParameter("optimization.ignore_parameter", bppdist.getParams(), "", "", true, false); bool ignoreBrLen = false; StringTokenizer st(paramListDesc, ","); while (st.hasMoreToken()) { try { string param = st.nextToken(); if (param == "BrLen") ignoreBrLen = true; else { if (allParameters.hasParameter(param)) { Parameter* p = &allParameters.getParameter(param); parametersToIgnore.addParameter(*p); } else ApplicationTools::displayWarning("Parameter '" + param + "' not found."); } } catch (ParameterNotFoundException& pnfe) { ApplicationTools::displayError("Parameter '" + pnfe.getParameter() + "' not found, and so can't be ignored!"); } } unsigned int nbEvalMax = ApplicationTools::getParameter("optimization.max_number_f_eval", bppdist.getParams(), 1000000); ApplicationTools::displayResult("Max # ML evaluations", TextTools::toString(nbEvalMax)); double tolerance = ApplicationTools::getDoubleParameter("optimization.tolerance", bppdist.getParams(), .000001); ApplicationTools::displayResult("Tolerance", TextTools::toString(tolerance)); //Here it is: ofstream warn("warnings", ios::out); shared_ptr wout = ApplicationTools::warning; ApplicationTools::warning.reset(new StlOutputStreamWrapper(&warn)); tree = OptimizationTools::buildDistanceTree(distEstimation, *distMethod, parametersToIgnore, !ignoreBrLen, type, tolerance, nbEvalMax, profiler, messenger, optVerbose); warn.close(); ApplicationTools::warning = wout; string matrixPath = ApplicationTools::getAFilePath("output.matrix.file", bppdist.getParams(), false, false, "", false); if (matrixPath != "none") { ApplicationTools::displayResult("Output matrix file", matrixPath); string matrixFormat = ApplicationTools::getAFilePath("output.matrix.format", bppdist.getParams(), false, false, "", false); string format = ""; bool extended = false; std::map unparsedArguments_; KeyvalTools::parseProcedure(matrixFormat, format, unparsedArguments_); if (unparsedArguments_.find("type") != unparsedArguments_.end()) { if (unparsedArguments_["type"] == "extended") { extended = true; } else if (unparsedArguments_["type"] == "classic") extended = false; else ApplicationTools::displayWarning("Argument '" + unparsedArguments_["type"] + "' for parameter 'Phylip#type' is unknown. " + "Default used instead: not extended."); } else ApplicationTools::displayWarning("Argument 'Phylip#type' not found. Default used instead: not extended."); ODistanceMatrix* odm = IODistanceMatrixFactory().createWriter(IODistanceMatrixFactory::PHYLIP_FORMAT, extended); odm->write(*distEstimation.getMatrix(), matrixPath, true); delete odm; } PhylogeneticsApplicationTools::writeTree(*tree, bppdist.getParams()); //Output some parameters: if (type == OptimizationTools::DISTANCEMETHOD_ITERATIONS) { // Write parameters to screen: ParameterList parameters = model->getParameters(); for (unsigned int i = 0; i < parameters.size(); i++) { ApplicationTools::displayResult(parameters[i].getName(), TextTools::toString(parameters[i].getValue())); } parameters = rDist->getParameters(); for (unsigned int i = 0; i < parameters.size(); i++) { ApplicationTools::displayResult(parameters[i].getName(), TextTools::toString(parameters[i].getValue())); } // Write parameters to file: string parametersFile = ApplicationTools::getAFilePath("output.estimates", bppdist.getParams(), false, false); if (parametersFile != "none") { ofstream out(parametersFile.c_str(), ios::out); parameters = model->getParameters(); for (unsigned int i = 0; i < parameters.size(); i++) { out << parameters[i].getName() << " = " << parameters[i].getValue() << endl; } parameters = rDist->getParameters(); for (unsigned int i = 0; i < parameters.size(); i++) { out << parameters[i].getName() << " = " << parameters[i].getValue() << endl; } out.close(); } } //Bootstrap: unsigned int nbBS = ApplicationTools::getParameter("bootstrap.number", bppdist.getParams(), 0); if(nbBS > 0) { ApplicationTools::displayResult("Number of bootstrap samples", TextTools::toString(nbBS)); bool approx = ApplicationTools::getBooleanParameter("bootstrap.approximate", bppdist.getParams(), true); ApplicationTools::displayResult("Use approximate bootstrap", TextTools::toString(approx ? "yes" : "no")); if(approx) { type = OptimizationTools::DISTANCEMETHOD_INIT; parametersToIgnore = allParameters; ignoreBrLen = true; } bool bootstrapVerbose = ApplicationTools::getBooleanParameter("bootstrap.verbose", bppdist.getParams(), false, "", true, false); string bsTreesPath = ApplicationTools::getAFilePath("bootstrap.output.file", bppdist.getParams(), false, false); ofstream *out = NULL; if(bsTreesPath != "none") { ApplicationTools::displayResult("Bootstrap trees stored in file", bsTreesPath); out = new ofstream(bsTreesPath.c_str(), ios::out); } Newick newick; vector bsTrees(nbBS); ApplicationTools::displayTask("Bootstrapping", true); for(unsigned int i = 0; i < nbBS; i++) { ApplicationTools::displayGauge(i, nbBS-1, '='); VectorSiteContainer * sample = SiteContainerTools::bootstrapSites(*sites); if(approx) model->setFreqFromData(*sample); distEstimation.setData(sample); bsTrees[i] = OptimizationTools::buildDistanceTree( distEstimation, *distMethod, parametersToIgnore, ignoreBrLen, type, tolerance, nbEvalMax, NULL, NULL, (bootstrapVerbose ? 1 : 0) ); if(out && i == 0) newick.write(*bsTrees[i], bsTreesPath, true); if(out && i > 0) newick.write(*bsTrees[i], bsTreesPath, false); delete sample; } if(out) out->close(); if(out) delete out; ApplicationTools::displayTaskDone(); ApplicationTools::displayTask("Compute bootstrap values"); TreeTools::computeBootstrapValues(*tree, bsTrees); ApplicationTools::displayTaskDone(); for(unsigned int i = 0; i < nbBS; i++) delete bsTrees[i]; //Write resulting tree: PhylogeneticsApplicationTools::writeTree(*tree, bppdist.getParams()); } delete alphabet; delete sites; delete distMethod; delete tree; bppdist.done();} catch(exception & e) { cout << e.what() << endl; return 1; } return 0; } bppsuite-2.4.1/bppSuite/bppML.cpp000066400000000000000000000771651333524216000167010ustar00rootroot00000000000000// // File: bppML.cpp // Created by: Julien Dutheil // Created on: Dec Sat 03 16:41 2005 // /* Copyright or © or Copr. Bio++ Development Team This software is a computer program whose purpose is to estimate phylogenies and evolutionary parameters from a dataset according to the maximum likelihood principle. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. */ // From the STL: #include #include #include using namespace std; // From bpp-core: #include #include #include #include #include #include #include #include #include #include #include #include // From bpp-seq: #include #include #include #include #include // From bpp-phyl: #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include using namespace bpp; /******************************************************************************/ void help() { (*ApplicationTools::message << "__________________________________________________________________________").endLine(); (*ApplicationTools::message << "bppml parameter1_name=parameter1_value parameter2_name=parameter2_value").endLine(); (*ApplicationTools::message << " ... param=option_file").endLine(); (*ApplicationTools::message).endLine(); (*ApplicationTools::message << " Refer to the Bio++ Program Suite Manual for a list of available options.").endLine(); (*ApplicationTools::message << "__________________________________________________________________________").endLine(); } int main(int args, char** argv) { cout << "******************************************************************" << endl; cout << "* Bio++ Maximum Likelihood Computation, version " << BPP_VERSION << " *" << endl; cout << "* *" << endl; cout << "* Authors: J. Dutheil Last Modif. " << BPP_REL_DATE << " *" << endl; cout << "* B. Boussau *" << endl; cout << "* L. Guéguen *" << endl; cout << "* M. Groussin *" << endl; cout << "******************************************************************" << endl; cout << endl; if (args == 1) { help(); return 0; } try { BppApplication bppml(args, argv, "BppML"); bppml.startTimer(); Alphabet* alphabet = SequenceApplicationTools::getAlphabet(bppml.getParams(), "", false); unique_ptr gCode; CodonAlphabet* codonAlphabet = dynamic_cast(alphabet); if (codonAlphabet) { string codeDesc = ApplicationTools::getStringParameter("genetic_code", bppml.getParams(), "Standard", "", true, true); ApplicationTools::displayResult("Genetic Code", codeDesc); gCode.reset(SequenceApplicationTools::getGeneticCode(codonAlphabet->getNucleicAlphabet(), codeDesc)); } ////////////////////////////////////////////// // DATA VectorSiteContainer* allSites = SequenceApplicationTools::getSiteContainer(alphabet, bppml.getParams()); VectorSiteContainer* sites = SequenceApplicationTools::getSitesToAnalyse(*allSites, bppml.getParams(), "", true, false); delete allSites; ApplicationTools::displayResult("Number of sequences", TextTools::toString(sites->getNumberOfSequences())); ApplicationTools::displayResult("Number of sites", TextTools::toString(sites->getNumberOfSites())); ///////////////////////////////////////// // TREE // Get the initial tree Tree* tree = 0; string initTreeOpt = ApplicationTools::getStringParameter("init.tree", bppml.getParams(), "user", "", false, 1); ApplicationTools::displayResult("Input tree", initTreeOpt); if (initTreeOpt == "user") { tree = PhylogeneticsApplicationTools::getTree(bppml.getParams()); ApplicationTools::displayResult("Number of leaves", TextTools::toString(tree->getNumberOfLeaves())); } else if (initTreeOpt == "random") { vector names = sites->getSequencesNames(); tree = TreeTemplateTools::getRandomTree(names); tree->setBranchLengths(1.); } else throw Exception("Unknown init tree method."); // Try to write the current tree to file. This will be overwritten by the optimized tree, // but allow to check file existence before running optimization! PhylogeneticsApplicationTools::writeTree(*tree, bppml.getParams()); // Setting branch lengths? string initBrLenMethod = ApplicationTools::getStringParameter("init.brlen.method", bppml.getParams(), "Input", "", true, 1); string cmdName; map cmdArgs; KeyvalTools::parseProcedure(initBrLenMethod, cmdName, cmdArgs); if (cmdName == "Input") { // Is the root has to be moved to the midpoint position along the branch that contains it ? If no, do nothing! bool midPointRootBrLengths = ApplicationTools::getBooleanParameter("midpoint_root_branch", cmdArgs, false, "", true, 2); if(midPointRootBrLengths) TreeTools::constrainedMidPointRooting(*tree); } else if (cmdName == "Equal") { double value = ApplicationTools::getDoubleParameter("value", cmdArgs, 0.1, "", true, 2); if (value <= 0) throw Exception("Value for branch length must be superior to 0"); ApplicationTools::displayResult("Branch lengths set to", value); tree->setBranchLengths(value); } else if (cmdName == "Clock") { TreeTools::convertToClockTree(*tree, tree->getRootId(), true); } else if (cmdName == "Grafen") { string grafenHeight = ApplicationTools::getStringParameter("height", cmdArgs, "input", "", true, 2); double h; if (grafenHeight == "input") { h = TreeTools::getHeight(*tree, tree->getRootId()); } else { h = TextTools::toDouble(grafenHeight); if (h <= 0) throw Exception("Height must be positive in Grafen's method."); } ApplicationTools::displayResult("Total height", TextTools::toString(h)); double rho = ApplicationTools::getDoubleParameter("rho", cmdArgs, 1., "", true, 2); ApplicationTools::displayResult("Grafen's rho", rho); TreeTools::computeBranchLengthsGrafen(*tree, rho); double nh = TreeTools::getHeight(*tree, tree->getRootId()); tree->scaleTree(h / nh); } else throw Exception("Method '" + initBrLenMethod + "' unknown for computing branch lengths."); ApplicationTools::displayResult("Branch lengths", cmdName); string treeWIdPath = ApplicationTools::getAFilePath("output.tree_ids.file", bppml.getParams(), false, false, "", true, "none", 1); if (treeWIdPath != "none") { TreeTemplate ttree(*tree); vector nodes = ttree.getNodes(); for (size_t i = 0; i < nodes.size(); i++) { if (nodes[i]->isLeaf()) nodes[i]->setName(TextTools::toString(nodes[i]->getId()) + "_" + nodes[i]->getName()); else nodes[i]->setBranchProperty("NodeId", BppString(TextTools::toString(nodes[i]->getId()))); } Newick treeWriter; treeWriter.enableExtendedBootstrapProperty("NodeId"); ApplicationTools::displayResult("Writing tagged tree to", treeWIdPath); treeWriter.write(ttree, treeWIdPath); delete tree; cout << "BppML's done." << endl; exit(0); } ///////////////////////// // MODEL & LIKELIHOOD // Check if likelihood bool computeLikelihood = ApplicationTools::getBooleanParameter("compute.likelihood", bppml.getParams(), true, "", false, 1); if (!computeLikelihood) { delete alphabet; delete sites; delete tree; cout << "BppML's done. Bye." << endl; return 0; } DiscreteRatesAcrossSitesTreeLikelihood* tl; string nhOpt = ApplicationTools::getStringParameter("nonhomogeneous", bppml.getParams(), "no", "", true, 1); ApplicationTools::displayResult("Heterogeneous model", nhOpt); bool checkTree = ApplicationTools::getBooleanParameter("input.tree.check_root", bppml.getParams(), true, "", true, 2); bool optimizeTopo = ApplicationTools::getBooleanParameter("optimization.topology", bppml.getParams(), false, "", true, 1); unsigned int nbBS = ApplicationTools::getParameter("bootstrap.number", bppml.getParams(), 0, "", true, 1); TransitionModel* model = 0; SubstitutionModelSet* modelSet = 0; DiscreteDistribution* rDist = 0; //////////// // If optimize topology if (optimizeTopo || nbBS > 0) { if (nhOpt != "no") throw Exception("Topology estimation with NH model not supported yet, sorry :("); model = PhylogeneticsApplicationTools::getTransitionModel(alphabet, gCode.get(), sites, bppml.getParams()); if (model->getName() != "RE08") SiteContainerTools::changeGapsToUnknownCharacters(*sites); if (model->getNumberOfStates() >= 2 * model->getAlphabet()->getSize()) { // Markov-modulated Markov model! rDist = new ConstantRateDistribution(); } else { rDist = PhylogeneticsApplicationTools::getRateDistribution(bppml.getParams()); } if (dynamic_cast(model) == 0) tl = new NNIHomogeneousTreeLikelihood(*tree, *sites, model, rDist, checkTree, true); else throw Exception("Topology estimation with Mixed model not supported yet, sorry :("); } ////////////////////// // If not topology optimization ///// homogeneous modeling else if (nhOpt == "no") { model = PhylogeneticsApplicationTools::getTransitionModel(alphabet, gCode.get(), sites, bppml.getParams()); if (model->getName() != "RE08") SiteContainerTools::changeGapsToUnknownCharacters(*sites); if (model->getNumberOfStates() >= 2 * model->getAlphabet()->getSize()) { // Markov-modulated Markov model! rDist = new ConstantRateDistribution(); } else { rDist = PhylogeneticsApplicationTools::getRateDistribution(bppml.getParams()); } string recursion = ApplicationTools::getStringParameter("likelihood.recursion", bppml.getParams(), "simple", "", true, 1); ApplicationTools::displayResult("Likelihood recursion", recursion); if (recursion == "simple") { string compression = ApplicationTools::getStringParameter("likelihood.recursion_simple.compression", bppml.getParams(), "recursive", "", true, 2); ApplicationTools::displayResult("Likelihood data compression", compression); if (compression == "simple") if (dynamic_cast(model)) tl = new RHomogeneousMixedTreeLikelihood(*tree, *sites, model, rDist, checkTree, true, false); else tl = new RHomogeneousTreeLikelihood(*tree, *sites, model, rDist, checkTree, true, false); else if (compression == "recursive") if (dynamic_cast(model) == 0) tl = new RHomogeneousTreeLikelihood(*tree, *sites, model, rDist, checkTree, true, true); else tl = new RHomogeneousMixedTreeLikelihood(*tree, *sites, model, rDist, checkTree, true, true); else throw Exception("Unknown likelihood data compression method: " + compression); } else if (recursion == "double") { if (dynamic_cast(model)) tl = new DRHomogeneousMixedTreeLikelihood(*tree, *sites, model, rDist, checkTree); else tl = new DRHomogeneousTreeLikelihood(*tree, *sites, model, rDist, checkTree); } else throw Exception("Unknown recursion option: " + recursion); } ///// one per branch modeling else if (nhOpt == "one_per_branch") { model = PhylogeneticsApplicationTools::getTransitionModel(alphabet, gCode.get(), sites, bppml.getParams()); if (model->getName() != "RE08") SiteContainerTools::changeGapsToUnknownCharacters(*sites); if (model->getNumberOfStates() >= 2 * model->getAlphabet()->getSize()) { // Markov-modulated Markov model! rDist = new ConstantRateDistribution(); } else { rDist = PhylogeneticsApplicationTools::getRateDistribution(bppml.getParams()); } vector rateFreqs; if (model->getNumberOfStates() != alphabet->getSize()) { // Markov-Modulated Markov Model... unsigned int n = static_cast(model->getNumberOfStates() / alphabet->getSize()); rateFreqs = vector(n, 1. / static_cast(n)); // Equal rates assumed for now, may be changed later (actually, in the most general case, // we should assume a rate distribution for the root also!!! } bool stationarity = ApplicationTools::getBooleanParameter("nonhomogeneous.stationarity", bppml.getParams(), false, "", false, 1); FrequenciesSet* rootFreqs = 0; std::map aliasFreqNames; if (!stationarity) { rootFreqs = PhylogeneticsApplicationTools::getRootFrequenciesSet(alphabet, gCode.get(), sites, bppml.getParams(), aliasFreqNames, rateFreqs); stationarity = !rootFreqs; string freqDescription = ApplicationTools::getStringParameter("nonhomogeneous.root_freq", bppml.getParams(), "", "", true, 1); if (freqDescription == "MVAprotein") { if (dynamic_cast(model)) { dynamic_cast(rootFreqs)->setModelName("MVAprotein"); dynamic_cast(rootFreqs)->initSet(dynamic_cast(model)); } else throw Exception("The MVAprotein frequencies set at the root can only be used if a COaLA model is used on branches."); } } ApplicationTools::displayBooleanResult("Stationarity assumed", stationarity); vector globalParameters = ApplicationTools::getVectorParameter("nonhomogeneous_one_per_branch.shared_parameters", bppml.getParams(), ',', ""); for (size_t i = 0; i < globalParameters.size(); i++) ApplicationTools::displayResult("Global parameter", globalParameters[i]); modelSet = SubstitutionModelSetTools::createNonHomogeneousModelSet(model, rootFreqs, tree, aliasFreqNames, globalParameters); model = 0; string recursion = ApplicationTools::getStringParameter("likelihood.recursion", bppml.getParams(), "simple", "", true, 1); ApplicationTools::displayResult("Likelihood recursion", recursion); if (recursion == "simple") { if (dynamic_cast(modelSet)!=NULL) tl = new RNonHomogeneousMixedTreeLikelihood(*tree, *sites, dynamic_cast(modelSet), rDist, true, true); else tl = new RNonHomogeneousTreeLikelihood(*tree, *sites, modelSet, rDist, true, true); } else if (recursion == "double") { if (dynamic_cast(modelSet)) throw Exception("Double recursion with non homogeneous mixed models is not implemented yet."); // tl = new DRNonHomogeneousMixedTreeLikelihood(*tree, *sites, modelSet, rDist, true); else tl = new DRNonHomogeneousTreeLikelihood(*tree, *sites, modelSet, rDist, true); } else throw Exception("Unknown recursion option: " + recursion); } /////// hand made modeling else if (nhOpt == "general") { modelSet = PhylogeneticsApplicationTools::getSubstitutionModelSet(alphabet, gCode.get(), sites, bppml.getParams()); if (modelSet->getModel(0)->getName() != "RE08") SiteContainerTools::changeGapsToUnknownCharacters(*sites); if (modelSet->getNumberOfStates() >= 2 * modelSet->getAlphabet()->getSize()) { // Markov-modulated Markov model! rDist = new ConstantRateDistribution(); } else { rDist = PhylogeneticsApplicationTools::getRateDistribution(bppml.getParams()); } string recursion = ApplicationTools::getStringParameter("likelihood.recursion", bppml.getParams(), "simple", "", true, 1); ApplicationTools::displayResult("Likelihood recursion", recursion); if (recursion == "simple") { if (dynamic_cast(modelSet)!=NULL) tl = new RNonHomogeneousMixedTreeLikelihood(*tree, *sites, dynamic_cast(modelSet), rDist, true, true); else tl = new RNonHomogeneousTreeLikelihood(*tree, *sites, modelSet, rDist, true, true); } else if (recursion == "double") if (dynamic_cast(modelSet)) throw Exception("Double recursion with non homogeneous mixed models is not implemented yet."); // tl = new DRNonHomogeneousMixedTreeLikelihood(*tree, *sites, modelSet, rDist, true); else tl = new DRNonHomogeneousTreeLikelihood(*tree, *sites, modelSet, rDist, true); else throw Exception("Unknown recursion option: " + recursion); } else throw Exception("Unknown option for nonhomogeneous: " + nhOpt); tl->initialize(); delete tree; //Listing parameters string paramNameFile = ApplicationTools::getAFilePath("output.parameter_names.file", bppml.getParams(), false, false, "", true, "none", 1); if (paramNameFile != "none") { ApplicationTools::displayResult("List parameters to", paramNameFile); ofstream pnfile(paramNameFile.c_str(), ios::out); ParameterList pl = tl->getParameters(); for (size_t i = 0; i < pl.size(); ++i) { pnfile << pl[i].getName() << endl; } pnfile.close(); cout << "BppML's done." << endl; exit(0); } //Check initial likelihood: double logL = tl->getValue(); if (std::isinf(logL)) { // This may be due to null branch lengths, leading to null likelihood! ApplicationTools::displayWarning("!!! Warning!!! Initial likelihood is zero."); ApplicationTools::displayWarning("!!! This may be due to branch length == 0."); ApplicationTools::displayWarning("!!! All null branch lengths will be set to 0.000001."); ParameterList pl = tl->getBranchLengthsParameters(); for (unsigned int i = 0; i < pl.size(); i++) { if (pl[i].getValue() < 0.000001) pl[i].setValue(0.000001); } tl->matchParametersValues(pl); logL = tl->getValue(); } ApplicationTools::displayResult("Initial log likelihood", TextTools::toString(-logL, 15)); if (std::isinf(logL)) { ApplicationTools::displayError("!!! Unexpected initial likelihood == 0."); if (codonAlphabet) { bool f = false; size_t s; for (size_t i = 0; i < sites->getNumberOfSites(); i++) { if (std::isinf(tl->getLogLikelihoodForASite(i))) { const Site& site = sites->getSite(i); s = site.size(); for (size_t j = 0; j < s; j++) { if (gCode->isStop(site.getValue(j))) { (*ApplicationTools::error << "Stop Codon at site " << site.getPosition() << " in sequence " << sites->getSequence(j).getName()).endLine(); f = true; } } } } if (f) exit(-1); } bool removeSaturated = ApplicationTools::getBooleanParameter("input.sequence.remove_saturated_sites", bppml.getParams(), false, "", true, 1); if (!removeSaturated) { ofstream debug ("DEBUG_likelihoods.txt", ios::out); for (size_t i = 0; i < sites->getNumberOfSites(); i++) { debug << "Position " << sites->getSite(i).getPosition() << " = " << tl->getLogLikelihoodForASite(i) << endl; } debug.close(); ApplicationTools::displayError("!!! Site-specific likelihood have been written in file DEBUG_likelihoods.txt ."); ApplicationTools::displayError("!!! 0 values (inf in log) may be due to computer overflow, particularily if datasets are big (>~500 sequences)."); ApplicationTools::displayError("!!! You may want to try input.sequence.remove_saturated_sites = yes to ignore positions with likelihood 0."); exit(1); } else { ApplicationTools::displayBooleanResult("Saturated site removal enabled", true); for (size_t i = sites->getNumberOfSites(); i > 0; --i) { if (std::isinf(tl->getLogLikelihoodForASite(i - 1))) { ApplicationTools::displayResult("Ignore saturated site", sites->getSite(i - 1).getPosition()); sites->deleteSite(i - 1); } } ApplicationTools::displayResult("Number of sites retained", sites->getNumberOfSites()); tl->setData(*sites); tl->initialize(); logL = tl->getValue(); if (std::isinf(logL)) { throw Exception("Likelihood is still 0 after saturated sites are removed! Looks like a bug..."); } ApplicationTools::displayResult("Initial log likelihood", TextTools::toString(-logL, 15)); } } tl = dynamic_cast( PhylogeneticsApplicationTools::optimizeParameters(tl, tl->getParameters(), bppml.getParams())); tree = new TreeTemplate(tl->getTree()); PhylogeneticsApplicationTools::writeTree(*tree, bppml.getParams()); // Write parameters to screen: ApplicationTools::displayResult("Log likelihood", TextTools::toString(-tl->getValue(), 15)); ParameterList parameters = tl->getSubstitutionModelParameters(); for (size_t i = 0; i < parameters.size(); i++) { ApplicationTools::displayResult(parameters[i].getName(), TextTools::toString(parameters[i].getValue())); } parameters = tl->getRateDistributionParameters(); for (size_t i = 0; i < parameters.size(); i++) { ApplicationTools::displayResult(parameters[i].getName(), TextTools::toString(parameters[i].getValue())); } // Checking convergence: PhylogeneticsApplicationTools::checkEstimatedParameters(tl->getParameters()); // Write parameters to file: string parametersFile = ApplicationTools::getAFilePath("output.estimates", bppml.getParams(), false, false, "none", 1); bool withAlias = ApplicationTools::getBooleanParameter("output.estimates.alias", bppml.getParams(), true, "", true, 0); ApplicationTools::displayResult("Output estimates to file", parametersFile); if (parametersFile != "none") { StlOutputStream out(new ofstream(parametersFile.c_str(), ios::out)); out << "# Log likelihood = "; out.setPrecision(20) << (-tl->getValue()); out.endLine(); out << "# Number of sites = "; out.setPrecision(20) << sites->getNumberOfSites(); out.endLine(); out.endLine(); out << "# Substitution model parameters:"; out.endLine(); if (modelSet) { modelSet->matchParametersValues(tl->getParameters()); PhylogeneticsApplicationTools::printParameters(modelSet, out, 1, withAlias); } else { model->matchParametersValues(tl->getParameters()); PhylogeneticsApplicationTools::printParameters(model, out, 1, withAlias); } out.endLine(); (out << "# Rate distribution parameters:").endLine(); rDist->matchParametersValues(tl->getParameters()); PhylogeneticsApplicationTools::printParameters(rDist, out, withAlias); } // Getting posterior rate class distribution: DiscreteDistribution* prDist = RASTools::getPosteriorRateDistribution(*tl); ApplicationTools::displayMessage("\nPosterior rate distribution for dataset:\n"); if (ApplicationTools::message) prDist->print(*ApplicationTools::message); ApplicationTools::displayMessage("\n"); delete prDist; // Write infos to file: string infosFile = ApplicationTools::getAFilePath("output.infos", bppml.getParams(), false, false); if (infosFile != "none") { ApplicationTools::displayResult("Alignment information logfile", infosFile); ofstream out(infosFile.c_str(), ios::out); // Get the rate class with maximum posterior probability: vector classes = tl->getRateClassWithMaxPostProbOfEachSite(); // Get the posterior rate, i.e. rate averaged over all posterior probabilities: Vdouble rates = tl->getPosteriorRateOfEachSite(); vector colNames; colNames.push_back("Sites"); colNames.push_back("is.complete"); colNames.push_back("is.constant"); colNames.push_back("lnL"); colNames.push_back("rc"); colNames.push_back("pr"); vector row(6); DataTable* infos = new DataTable(colNames); for (unsigned int i = 0; i < sites->getNumberOfSites(); i++) { double lnL = tl->getLogLikelihoodForASite(i); const Site* currentSite = &sites->getSite(i); int currentSitePosition = currentSite->getPosition(); string isCompl = "NA"; string isConst = "NA"; try { isCompl = (SiteTools::isComplete(*currentSite) ? "1" : "0"); } catch(EmptySiteException& ex) {} try { isConst = (SiteTools::isConstant(*currentSite) ? "1" : "0"); } catch(EmptySiteException& ex) {} row[0] = (string("[" + TextTools::toString(currentSitePosition) + "]")); row[1] = isCompl; row[2] = isConst; row[3] = TextTools::toString(lnL); row[4] = TextTools::toString(classes[i]); row[5] = TextTools::toString(rates[i]); infos->addRow(row); } DataTable::write(*infos, out, "\t"); delete infos; } // Bootstrap: string optimizeClock = ApplicationTools::getStringParameter("optimization.clock", bppml.getParams(), "None", "", true, 1); if (nbBS > 0 && optimizeClock != "None") { ApplicationTools::displayError("Bootstrap is not supported with clock trees."); } if (nbBS > 0 && optimizeClock == "None") { ApplicationTools::displayResult("Number of bootstrap samples", TextTools::toString(nbBS)); bool approx = ApplicationTools::getBooleanParameter("bootstrap.approximate", bppml.getParams(), true, "", true, 2); ApplicationTools::displayBooleanResult("Use approximate bootstrap", approx); bool bootstrapVerbose = ApplicationTools::getBooleanParameter("bootstrap.verbose", bppml.getParams(), false, "", true, 2); const Tree* initTree = tree; if (!bootstrapVerbose) bppml.getParam("optimization.verbose") = "0"; bppml.getParam("optimization.profiler") = "none"; bppml.getParam("optimization.messageHandler") = "none"; if (!optimizeTopo) { bppml.getParam("optimization.topology") = "yes"; tl = dynamic_cast( PhylogeneticsApplicationTools::optimizeParameters(tl, tl->getParameters(), bppml.getParams(), "", true, false)); initTree = &tl->getTree(); } string bsTreesPath = ApplicationTools::getAFilePath("bootstrap.output.file", bppml.getParams(), false, false); ofstream* out = 0; if (bsTreesPath != "none") { ApplicationTools::displayResult("Bootstrap trees stored in file", bsTreesPath); out = new ofstream(bsTreesPath.c_str(), ios::out); } Newick newick; ParameterList paramsToIgnore = tl->getSubstitutionModelParameters(); paramsToIgnore.addParameters(tl->getRateDistributionParameters()); ApplicationTools::displayTask("Bootstrapping", true); vector bsTrees(nbBS); for (unsigned int i = 0; i < nbBS; i++) { ApplicationTools::displayGauge(i, nbBS - 1, '='); VectorSiteContainer* sample = SiteContainerTools::bootstrapSites(*sites); if (!approx) { model->setFreqFromData(*sample); } if (dynamic_cast(model) != NULL) throw Exception("Bootstrap estimation with Mixed model not supported yet, sorry :("); NNIHomogeneousTreeLikelihood* tlRep = new NNIHomogeneousTreeLikelihood(*initTree, *sample, model, rDist, true, false); tlRep->initialize(); ParameterList parametersRep = tlRep->getParameters(); if (approx) { parametersRep.deleteParameters(paramsToIgnore.getParameterNames()); } tlRep = dynamic_cast( PhylogeneticsApplicationTools::optimizeParameters(tlRep, parametersRep, bppml.getParams(), "", true, false)); bsTrees[i] = new TreeTemplate(tlRep->getTree()); if (out && i == 0) newick.write(*bsTrees[i], bsTreesPath, true); if (out && i > 0) newick.write(*bsTrees[i], bsTreesPath, false); delete tlRep; delete sample; } if (out) out->close(); if (out) delete out; ApplicationTools::displayTaskDone(); ApplicationTools::displayTask("Compute bootstrap values"); TreeTools::computeBootstrapValues(*tree, bsTrees); ApplicationTools::displayTaskDone(); for (unsigned int i = 0; i < nbBS; i++) { delete bsTrees[i]; } // Write resulting tree: PhylogeneticsApplicationTools::writeTree(*tree, bppml.getParams()); } delete alphabet; delete sites; if (model) delete model; if (modelSet) delete modelSet; delete rDist; delete tl; delete tree; bppml.done(); } catch (exception& e) { cout << e.what() << endl; return 1; } return 0; } bppsuite-2.4.1/bppSuite/bppMixedLikelihoods.cpp000066400000000000000000000504071333524216000216140ustar00rootroot00000000000000// // File: bppMixedLikelihoods.cpp // Created by: Laurent Guéguen // Created on: lundi 12 novembre 2012, à 07h 02 // /* Copyright or © or Copr. Bio++ Development Team This software is a computer program whose purpose is to estimate phylogenies and evolutionary parameters from a dataset according to the maximum likelihood principle. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. */ // From the STL: #include #include using namespace std; // From bpp-core: #include #include #include #include #include #include #include #include #include #include #include // From bpp-seq: #include #include #include #include #include #include // From bpp-phyl: #include #include #include #include #include #include #include #include #include #include #include #include #include using namespace bpp; /******************************************************************************/ void help() { (*ApplicationTools::message << "__________________________________________________________________________").endLine(); (*ApplicationTools::message << "bppmixedlikelihoods parameter1_name=parameter1_value ").endLine(); (*ApplicationTools::message << " parameter2_name=parameter2_value ... param=option_file").endLine(); (*ApplicationTools::message).endLine(); (*ApplicationTools::message << " Refer to the Bio++ Program Suite Manual for a list of available options.").endLine(); (*ApplicationTools::message << "__________________________________________________________________________").endLine(); } int main(int args, char** argv) { cout << "******************************************************************" << endl; cout << "* Bio++ Computation of site likelihoods inside mixed models *" << endl; cout << "* Version " << BPP_VERSION << ". *" << endl; cout << "* Author: L. Guéguen Last Modif.: " << BPP_REL_DATE << " *" << endl; cout << "******************************************************************" << endl; cout << endl; if (args == 1) { help(); return 0; } try { BppApplication bppmixedlikelihoods(args, argv, "BppMixedLikelihoods"); bppmixedlikelihoods.startTimer(); Alphabet* alphabet = SequenceApplicationTools::getAlphabet(bppmixedlikelihoods.getParams(), "", false); unique_ptr gCode; CodonAlphabet* codonAlphabet = dynamic_cast(alphabet); if (codonAlphabet) { string codeDesc = ApplicationTools::getStringParameter("genetic_code", bppmixedlikelihoods.getParams(), "Standard", "", true, true); ApplicationTools::displayResult("Genetic Code", codeDesc); gCode.reset(SequenceApplicationTools::getGeneticCode(codonAlphabet->getNucleicAlphabet(), codeDesc)); } // get the data VectorSiteContainer* allSites = SequenceApplicationTools::getSiteContainer(alphabet, bppmixedlikelihoods.getParams()); VectorSiteContainer* sites = SequenceApplicationTools::getSitesToAnalyse(*allSites, bppmixedlikelihoods.getParams(), "", true, false); delete allSites; ApplicationTools::displayResult("Number of sequences", TextTools::toString(sites->getNumberOfSequences())); ApplicationTools::displayResult("Number of sites", TextTools::toString(sites->getNumberOfSites())); // Get the tree Tree* tree = PhylogeneticsApplicationTools::getTree(bppmixedlikelihoods.getParams()); ApplicationTools::displayResult("Number of leaves", TextTools::toString(tree->getNumberOfLeaves())); AbstractDiscreteRatesAcrossSitesTreeLikelihood* tl; string nhOpt = ApplicationTools::getStringParameter("nonhomogeneous", bppmixedlikelihoods.getParams(), "no", "", true, false); ApplicationTools::displayResult("Heterogeneous model", nhOpt); MixedSubstitutionModel* model = 0; MixedSubstitutionModelSet* modelSet = 0; DiscreteDistribution* rDist = 0; if (nhOpt == "no") { model = dynamic_cast(PhylogeneticsApplicationTools::getSubstitutionModel(alphabet, gCode.get(), sites, bppmixedlikelihoods.getParams())); if (model == 0) { cout << "Model is not a Mixed model" << endl; exit(0); } SiteContainerTools::changeGapsToUnknownCharacters(*sites); if (model->getNumberOfStates() > model->getAlphabet()->getSize()) { // Markov-modulated Markov model! rDist = new ConstantRateDistribution(); } else { rDist = PhylogeneticsApplicationTools::getRateDistribution(bppmixedlikelihoods.getParams()); } tl = new RHomogeneousMixedTreeLikelihood(*tree, *sites, model, rDist, true); } else if (nhOpt == "one_per_branch") { model = dynamic_cast(PhylogeneticsApplicationTools::getSubstitutionModel(alphabet, gCode.get(), sites, bppmixedlikelihoods.getParams())); if (model == 0) { cout << "Model is not a Mixed model" << endl; exit(0); } SiteContainerTools::changeGapsToUnknownCharacters(*sites); if (model->getNumberOfStates() > model->getAlphabet()->getSize()) { // Markov-modulated Markov model! rDist = new ConstantRateDistribution(); } else { rDist = PhylogeneticsApplicationTools::getRateDistribution(bppmixedlikelihoods.getParams()); } vector rateFreqs; if (model->getNumberOfStates() != alphabet->getSize()) { // Markov-Modulated Markov Model... unsigned int n = (unsigned int)(model->getNumberOfStates() / alphabet->getSize()); rateFreqs = vector(n, 1. / (double)n); // Equal rates assumed for now, may be changed later (actually, in the most general case, // we should assume a rate distribution for the root also!!! } std::map aliasFreqNames; FrequenciesSet* rootFreqs = PhylogeneticsApplicationTools::getRootFrequenciesSet(alphabet, gCode.get(), sites, bppmixedlikelihoods.getParams(), aliasFreqNames, rateFreqs); vector globalParameters = ApplicationTools::getVectorParameter("nonhomogeneous_one_per_branch.shared_parameters", bppmixedlikelihoods.getParams(), ',', ""); modelSet = dynamic_cast(SubstitutionModelSetTools::createNonHomogeneousModelSet(model, rootFreqs, tree, aliasFreqNames, globalParameters)); model = 0; tl = new RNonHomogeneousMixedTreeLikelihood(*tree, *sites, modelSet, rDist, true); } else if (nhOpt == "general") { modelSet = dynamic_cast(PhylogeneticsApplicationTools::getSubstitutionModelSet(alphabet, gCode.get(), sites, bppmixedlikelihoods.getParams())); if (modelSet == 0) { cout << "Missing a Mixed model" << endl; exit(0); } SiteContainerTools::changeGapsToUnknownCharacters(*sites); if (modelSet->getNumberOfStates() > modelSet->getAlphabet()->getSize()) { // Markov-modulated Markov model! rDist = new ConstantDistribution(1.); } else { rDist = PhylogeneticsApplicationTools::getRateDistribution(bppmixedlikelihoods.getParams()); } tl = new RNonHomogeneousMixedTreeLikelihood(*tree, *sites, modelSet, rDist, true); } else throw Exception("Unknown option for nonhomogeneous: " + nhOpt); tl->initialize(); double logL = tl->getValue(); if (std::isinf(logL)) { // This may be due to null branch lengths, leading to null likelihood! ApplicationTools::displayWarning("!!! Warning!!! Likelihood is zero."); ApplicationTools::displayWarning("!!! This may be due to branch length == 0."); ApplicationTools::displayWarning("!!! All null branch lengths will be set to 0.000001."); ParameterList pl = tl->getBranchLengthsParameters(); for (unsigned int i = 0; i < pl.size(); i++) { if (pl[i].getValue() < 0.000001) pl[i].setValue(0.000001); } tl->matchParametersValues(pl); logL = tl->getValue(); } if (std::isinf(logL)) { ApplicationTools::displayError("!!! Unexpected likelihood == 0."); ApplicationTools::displayError("!!! Looking at each site:"); for (unsigned int i = 0; i < sites->getNumberOfSites(); i++) { (*ApplicationTools::error << "Site " << sites->getSite(i).getPosition() << "\tlog likelihood = " << tl->getLogLikelihoodForASite(i)).endLine(); } ApplicationTools::displayError("!!! 0 values (inf in log) may be due to computer overflow, particularily if datasets are big (>~500 sequences)."); exit(-1); } // Write parameters to screen: ApplicationTools::displayResult("Log likelihood", TextTools::toString(tl->getValue(), 15)); ParameterList parameters = tl->getSubstitutionModelParameters(); for (unsigned int i = 0; i < parameters.size(); i++) { ApplicationTools::displayResult(parameters[i].getName(), TextTools::toString(parameters[i].getValue())); } parameters = tl->getRateDistributionParameters(); for (unsigned int i = 0; i < parameters.size(); i++) { ApplicationTools::displayResult(parameters[i].getName(), TextTools::toString(parameters[i].getValue())); } // ///////////////////////////////////////////// // Getting likelihoods per submodel string outputFile; outputFile = ApplicationTools::getAFilePath("output.likelihoods.file", bppmixedlikelihoods.getParams(), true, false); ApplicationTools::displayResult("Output file for likelihoods", outputFile); ofstream out(outputFile.c_str(), ios::out); size_t nSites = sites->getNumberOfSites(); size_t nummodel = ApplicationTools::getParameter("likelihoods.model_number", bppmixedlikelihoods.getParams(), 1, "", true, true); string parname = ApplicationTools::getStringParameter("likelihoods.parameter_name", bppmixedlikelihoods.getParams(), "", "", true, false); if (modelSet && ((nummodel <= 0) || (nummodel > modelSet->getNumberOfModels()))) { ApplicationTools::displayError("Bad number of model " + TextTools::toString(nummodel) + "."); exit(-1); } MixedSubstitutionModel* p0 = dynamic_cast(model ? model : modelSet->getModel(nummodel - 1)); if (!p0) { ApplicationTools::displayError("Model " + TextTools::toString(nummodel) + " is not a Mixed Model."); exit(-1); } const AbstractBiblioMixedSubstitutionModel* ptmp = dynamic_cast(p0); if (ptmp) { p0 = ptmp->getMixedModel().clone(); if (nhOpt == "no") model = p0; else { modelSet->replaceModel(nummodel-1, p0); modelSet->isFullySetUpFor(*tree); } } ////////////////////////////////////////////////// // Case of a MixtureOfSubstitutionModels MixtureOfSubstitutionModels* pMSM = dynamic_cast(p0); if (pMSM) { vector colNames; colNames.push_back("Sites"); size_t nummod = pMSM->getNumberOfModels(); for (unsigned int i = 0; i < nummod; i++) { colNames.push_back(pMSM->getNModel(i)->getName()); } DataTable* rates = new DataTable(nSites, colNames.size()); rates->setColumnNames(colNames); for (unsigned int i = 0; i < nSites; i++) { const Site* currentSite = &sites->getSite(i); int currentSitePosition = currentSite->getPosition(); (*rates)(i, "Sites") = string("[" + TextTools::toString(currentSitePosition) + "]"); } Vdouble vprob = pMSM->getProbabilities(); for (unsigned int i = 0; i < nummod; i++) { string modname = pMSM->getNModel(i)->getName(); for (unsigned int j = 0; j < nummod; j++) { pMSM->setNProbability(j, (j == i) ? 1 : 0); } if (tl) delete tl; if (nhOpt == "no") tl = new RHomogeneousMixedTreeLikelihood(*tree, *sites, model, rDist, true, false, true); else tl = new RNonHomogeneousMixedTreeLikelihood(*tree, *sites, modelSet, rDist, false, true); tl->initialize(); logL = tl->getValue(); Vdouble Vd = tl->getLogLikelihoodForEachSite(); for (unsigned int j = 0; j < nSites; j++) { (*rates)(j, modname) = TextTools::toString(Vd[j]); } ApplicationTools::displayMessage("\n"); ApplicationTools::displayMessage("Model " + modname + ":"); ApplicationTools::displayResult("Log likelihood", TextTools::toString(tl->getValue(), 15)); ApplicationTools::displayResult("Probability", TextTools::toString(vprob[i], 15)); } DataTable::write(*rates, out, "\t"); } ////////////////////////////////////////////////// // Case of a MixtureOfASubstitutionModel else { MixtureOfASubstitutionModel* pMSM2 = dynamic_cast(p0); if (pMSM2 != NULL) { size_t nummod = pMSM2->getNumberOfModels(); if (parname == "") { ParameterList pl=pMSM2->getParameters(); for (size_t i2 = 0; i2 < pl.size(); i2++) { string pl2n = pl[i2].getName(); if (dynamic_cast(pMSM2->getDistribution(pl2n))==NULL) { parname=pl2n; while (parname.size()>0 && pMSM2->getDistribution(parname)==NULL) parname=pl2n.substr(0,pl2n.rfind("_")); if (parname.size()>0){ ApplicationTools::displayResult("likelihoods.parameter_name", parname); break; } } } } if (parname == "") { ApplicationTools::displayError("Argument likelihoods.parameter_name is required."); exit(-1); } vector< Vint > vvnmod; size_t i2 = 0; while (i2 < nummod) { string par2 = parname + "_" + TextTools::toString(i2 + 1); Vint vnmod = pMSM2->getSubmodelNumbers(par2); if (vnmod.size() == 0) break; vvnmod.push_back(vnmod); i2++; } size_t nbcl = vvnmod.size(); if (nbcl==0) throw Exception("Parameter " + parname + " is not mixed."); Vdouble vprob = pMSM2->getProbabilities(); vector > vvprob; vector vsprob; for (size_t i = 0; i < nbcl; i++) { vector vprob2; for (size_t j = 0; j < vvnmod[i].size(); j++) { vprob2.push_back(vprob[static_cast(vvnmod[i][j])]); } vvprob.push_back(vprob2); vsprob.push_back(VectorTools::sum(vvprob[i])); } vector colNames; colNames.push_back("Sites"); Vdouble dval; for (size_t i = 0; i < nbcl; i++) { SubstitutionModel* pSM = pMSM2->getNModel(static_cast(vvnmod[i][0])); double valPar = pSM->getParameterValue(pSM->getParameterNameWithoutNamespace(parname)); dval.push_back(valPar); colNames.push_back("Ll_" + parname + "=" + TextTools::toString(valPar)); } for (size_t i = 0; i < nbcl; i++) colNames.push_back("Pr_" + parname + "=" + TextTools::toString(dval[i])); colNames.push_back("mean"); DataTable* rates = new DataTable(nSites, colNames.size()); rates->setColumnNames(colNames); for (size_t i = 0; i < nSites; i++) { const Site* currentSite = &sites->getSite(i); int currentSitePosition = currentSite->getPosition(); (*rates)(i,"Sites")=TextTools::toString(currentSitePosition); } VVdouble vvd; vector vRates = pMSM2->getVRates(); for (size_t i = 0; i < nbcl; ++i) { string par2 = parname + "_" + TextTools::toString(i + 1); for (unsigned int j = 0; j < nummod; ++j) pMSM2->setNProbability(j, 0); for (size_t j = 0; j < vvprob[i].size(); ++j) pMSM2->setNProbability(static_cast(vvnmod[i][j]), vvprob[i][j] / vsprob[i]); if (tl) delete tl; if (nhOpt == "no") tl = new RHomogeneousMixedTreeLikelihood(*tree, *sites, model, rDist, true, false, true); else tl = new RNonHomogeneousMixedTreeLikelihood(*tree, *sites, modelSet, rDist, false, true); tl->initialize(); logL = tl->getValue(); Vdouble vd = tl->getLogLikelihoodForEachSite(); for (unsigned int j = 0; j < nSites; j++) (*rates)(j, i + 1) = TextTools::toString(vd[j]); vvd.push_back(vd); ApplicationTools::displayMessage("\n"); ApplicationTools::displayMessage("Parameter " + par2 + "=" + TextTools::toString(dval[i]) + " with rate=" + TextTools::toString(vRates[i])); ApplicationTools::displayResult("Log likelihood", TextTools::toString(tl->getValue(), 15)); ApplicationTools::displayResult("Probability", TextTools::toString(vsprob[i], 15)); } for (size_t j = 0; j < nSites; j++) { Vdouble vd; for (size_t i = 0; i < nbcl; i++) vd.push_back(std::log(vsprob[i])+vvd[i][j]); VectorTools::logNorm(vd); for (size_t i = 0; i < nbcl; i++) (*rates)(j,nbcl + i + 1) = TextTools::toString(std::exp(vd[i])); (*rates)(j, 2 * nbcl + 1) = TextTools::toString(VectorTools::sumExp(vd, dval)); } DataTable::write(*rates, out, "\t"); } } delete alphabet; delete sites; if (model) delete model; if (modelSet) delete modelSet; delete rDist; delete tl; delete tree; ApplicationTools::displayMessage("\n"); bppmixedlikelihoods.done(); } catch (exception& e) { cout << e.what() << endl; return 1; } return 0; } bppsuite-2.4.1/bppSuite/bppPars.cpp000066400000000000000000000175771333524216000172770ustar00rootroot00000000000000// // File: bppPars.cpp // Created by: Julien Dutheil // Created on: May Sat 05 15:09 2007 // From file bppML.cpp // /* Copyright or © or Copr. Bio++ Development Team This software is a computer program whose purpose is to estimate phylogenies and evolutionary parameters from a dataset according to the maximum likelihood principle. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. */ // From the STL: #include #include using namespace std; // From bpp-core: #include #include #include #include #include // From bpp-seq: #include #include #include #include #include // From bpp-phyl: #include #include #include #include #include using namespace bpp; void help() { (*ApplicationTools::message << "__________________________________________________________________________").endLine(); (*ApplicationTools::message << "bpppars parameter1_name=parameter1_value parameter2_name=parameter2_value").endLine(); (*ApplicationTools::message << " ... param=option_file").endLine(); (*ApplicationTools::message).endLine(); (*ApplicationTools::message << " Refer to the Bio++ Program Suite Manual for list of available options.").endLine(); (*ApplicationTools::message << "__________________________________________________________________________").endLine(); } int main(int args, char ** argv) { cout << "******************************************************************" << endl; cout << "* Bio++ Parsimony Methods, version " << BPP_VERSION << " *" << endl; cout << "* Author: J. Dutheil Created 05/05/07 *" << endl; cout << "* Last Modif. " << BPP_REL_DATE << " *" << endl; cout << "******************************************************************" << endl; cout << endl; if (args == 1) { help(); return 0; } try { BppApplication bpppars(args, argv, "BppPars"); bpppars.startTimer(); Alphabet* alphabet = SequenceApplicationTools::getAlphabet(bpppars.getParams(), "", false); bool includeGaps = ApplicationTools::getBooleanParameter("use.gaps", bpppars.getParams(), false, "", false, false); ApplicationTools::displayBooleanResult("Use gaps", includeGaps); VectorSiteContainer* allSites = SequenceApplicationTools::getSiteContainer(alphabet, bpppars.getParams()); VectorSiteContainer* sites = SequenceApplicationTools::getSitesToAnalyse(* allSites, bpppars.getParams(), "", true, !includeGaps, true); delete allSites; ApplicationTools::displayResult("Number of sequences", TextTools::toString(sites->getNumberOfSequences())); ApplicationTools::displayResult("Number of sites", TextTools::toString(sites->getNumberOfSites())); // Get the initial tree Tree* tree = 0; string initTreeOpt = ApplicationTools::getStringParameter("init.tree", bpppars.getParams(), "user", "", false, false); ApplicationTools::displayResult("Input tree", initTreeOpt); if (initTreeOpt == "user") { tree = PhylogeneticsApplicationTools::getTree(bpppars.getParams()); ApplicationTools::displayResult("Number of leaves", TextTools::toString(tree->getNumberOfLeaves())); } else if (initTreeOpt == "random") { vector names = sites->getSequencesNames(); tree = TreeTemplateTools::getRandomTree(names, false); tree->setBranchLengths(1.); } else throw Exception("Unknown init tree method."); ApplicationTools::displayTask("Initializing parsimony"); DRTreeParsimonyScore* tp = new DRTreeParsimonyScore(*tree, *sites, false, includeGaps); delete tree; ApplicationTools::displayTaskDone(); double score = tp->getScore(); ApplicationTools::displayResult("Initial parsimony score", TextTools::toString(score, 15)); bool optTopo = ApplicationTools::getBooleanParameter("optimization.topology", bpppars.getParams(), false); ApplicationTools::displayResult("Optimize topology", optTopo ? "yes" : "no"); if (optTopo) { tp = OptimizationTools::optimizeTreeNNI(tp, 1); score = tp->getScore(); ApplicationTools::displayResult("Final parsimony score", TextTools::toString(score, 15)); } tree = new TreeTemplate(tp->getTree()); PhylogeneticsApplicationTools::writeTree(*tree, bpppars.getParams()); //Bootstrap: unsigned int nbBS = ApplicationTools::getParameter("bootstrap.number", bpppars.getParams(), 0); if (nbBS > 0) { ApplicationTools::displayResult("Number of bootstrap samples", TextTools::toString(nbBS)); const Tree* initTree = tree; if (!optTopo) { tp = OptimizationTools::optimizeTreeNNI(tp, 1); initTree = &tp->getTree(); } string bsTreesPath = ApplicationTools::getAFilePath("bootstrap.output.file", bpppars.getParams(), false, false); ofstream *out = 0; if (bsTreesPath != "none") { ApplicationTools::displayResult("Bootstrap trees stored in file", bsTreesPath); out = new ofstream(bsTreesPath.c_str(), ios::out); } Newick newick; ApplicationTools::displayTask("Bootstrapping", true); vector bsTrees(nbBS); for (unsigned int i = 0; i < nbBS; i++) { ApplicationTools::displayGauge(i, nbBS - 1, '='); VectorSiteContainer* sample = SiteContainerTools::bootstrapSites(*sites); DRTreeParsimonyScore* tpRep = new DRTreeParsimonyScore(*initTree, *sample, false); tpRep = OptimizationTools::optimizeTreeNNI(tpRep, 0); bsTrees[i] = new TreeTemplate(tpRep->getTree()); if (out && i==0) newick.write(*bsTrees[i], bsTreesPath, true); if (out && i>0) newick.write(*bsTrees[i], bsTreesPath, false); delete tpRep; delete sample; } if(out) out->close(); if(out) delete out; ApplicationTools::displayTaskDone(); ApplicationTools::displayTask("Compute bootstrap values", true); TreeTools::computeBootstrapValues(*tree, bsTrees); ApplicationTools::displayTaskDone(); for (unsigned int i = 0; i < nbBS; i++) delete bsTrees[i]; //Write resulting tree: PhylogeneticsApplicationTools::writeTree(*tree, bpppars.getParams()); } delete sites; delete tp; delete alphabet; bpppars.done(); } catch (exception & e) { cout << e.what() << endl; return 1; } return 0; } bppsuite-2.4.1/bppSuite/bppPopStats.cpp000066400000000000000000000730331333524216000201340ustar00rootroot00000000000000// // File: bppPopStats.cpp // Created by: Julien Dutheil // Created on: Jun Wed 24 12:04 2015 // /* Copyright or © or Copr. Bio++ Development Team This software is a computer program whose purpose is to simulate sequence data according to a phylogenetic tree and an evolutionary model. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. */ // From the STL: #include #include #include #include #include using namespace std; // From bpp-core: #include #include #include #include #include // From bpp-seq: #include #include #include #include #include // From bpp-phyl: #include #include #include #include #include #include #include #include #include // From bpp-popgen #include #include #include using namespace bpp; void help() { (*ApplicationTools::message << "__________________________________________________________________________").endLine(); (*ApplicationTools::message << "bpppopstats parameter1_name=parameter1_value").endLine(); (*ApplicationTools::message << " parameter2_name=parameter2_value ... param=option_file").endLine(); (*ApplicationTools::message).endLine(); (*ApplicationTools::message << " Refer to the Bio++ Program Suite Manual for a list of available options.").endLine(); (*ApplicationTools::message << "__________________________________________________________________________").endLine(); } int main(int args, char** argv) { cout << "******************************************************************" << endl; cout << "* Bio++ Population Statistics, version " << BPP_VERSION << " *" << endl; cout << "* Author: J. Dutheil Last Modif. " << BPP_REL_DATE << " *" << endl; cout << "******************************************************************" << endl; cout << endl; if (args == 1) { help(); return 0; } BppApplication bpppopstats(args, argv, "BppPopStats"); bpppopstats.startTimer(); string logFile = ApplicationTools::getAFilePath("logfile", bpppopstats.getParams(), false, false); unique_ptr cLog; if (logFile != "none") cLog.reset(new ofstream(logFile.c_str(), ios::out)); //This counts instances of each tool, in case one is used several times, for instance with different options: map toolCounter; try { // Get alphabet Alphabet* alphabet = SequenceApplicationTools::getAlphabet(bpppopstats.getParams(), "", false, true, true); // Get the genetic code, if codon alphabet unique_ptr gCode; CodonAlphabet* codonAlphabet = dynamic_cast(alphabet); if (codonAlphabet) { string codeDesc = ApplicationTools::getStringParameter("genetic_code", bpppopstats.getParams(), "Standard", "", true, true); ApplicationTools::displayResult("Genetic Code", codeDesc); gCode.reset(SequenceApplicationTools::getGeneticCode(codonAlphabet->getNucleicAlphabet(), codeDesc)); } unique_ptr psc; if (ApplicationTools::parameterExists("input.sequence.file.ingroup", bpppopstats.getParams())) { // Get the ingroup alignment: unique_ptr sitesIn(SequenceApplicationTools::getSiteContainer(alphabet, bpppopstats.getParams(), ".ingroup", false, true)); psc.reset(new PolymorphismSequenceContainer(*sitesIn)); if (ApplicationTools::parameterExists("input.sequence.file.outgroup", bpppopstats.getParams())) { // Get the outgroup alignment: unique_ptr sitesOut(SequenceApplicationTools::getSiteContainer(alphabet, bpppopstats.getParams(), ".outgroup", false, true)); SequenceContainerTools::append(*psc, *sitesOut); for (size_t i = sitesIn->getNumberOfSequences(); i < psc->getNumberOfSequences(); ++i) { psc->setAsOutgroupMember(i); } } } else { //Everything in one file unique_ptr sites(SequenceApplicationTools::getSiteContainer(alphabet, bpppopstats.getParams(), "", false, true)); psc.reset(new PolymorphismSequenceContainer(*sites)); if (ApplicationTools::parameterExists("input.sequence.outgroup.index", bpppopstats.getParams())) { vector outgroups = ApplicationTools::getVectorParameter("input.sequence.outgroup.index", bpppopstats.getParams(), ',', ""); for (auto g : outgroups) { psc->setAsOutgroupMember(g-1); } } if (ApplicationTools::parameterExists("input.sequence.outgroup.name", bpppopstats.getParams())) { vector outgroups = ApplicationTools::getVectorParameter("input.sequence.outgroup.name", bpppopstats.getParams(), ',', ""); for (auto g : outgroups) { ApplicationTools::displayResult("Sequence from outgroup", g); psc->setAsOutgroupMember(g); } } } // Take care of stop codons: string stopCodonOpt = ApplicationTools::getStringParameter("input.sequence.stop_codons_policy", bpppopstats.getParams(), "Keep", "", true, true); ApplicationTools::displayResult("Stop codons policy", stopCodonOpt); if (stopCodonOpt == "Keep") { //do nothing } else if (stopCodonOpt == "RemoveIfLast") { if (CodonSiteTools::hasStop(psc->getSite(psc->getNumberOfSites() - 1), *gCode)) { psc->deleteSite(psc->getNumberOfSites() - 1); ApplicationTools::displayMessage("Info: last site contained a stop codon and was discarded."); if (logFile != "none") *cLog << "# Info: last site contained a stop codon and was discarded." << endl; } } else if (stopCodonOpt == "RemoveAll") { size_t l1 = psc->getNumberOfSites(); SiteContainerTools::removeStopCodonSites(*psc, *gCode); size_t l2 = psc->getNumberOfSites(); if (l2 != l1) { ApplicationTools::displayMessage("Info: discarded " + TextTools::toString(l1 - l2) + " sites with stop codons."); if (logFile != "none") *cLog << "# Info: discarded " << (l1 - l2) << " sites with stop codons." << endl; } } else { throw Exception("Unrecognized option for input.sequence.stop_codons_policy: " + stopCodonOpt); } shared_ptr pscIn; shared_ptr pscOut; if (psc->hasOutgroup()) { pscIn.reset(PolymorphismSequenceContainerTools::extractIngroup(*psc)); pscOut.reset(PolymorphismSequenceContainerTools::extractOutgroup(*psc)); } else { pscIn = std::move(psc); } ApplicationTools::displayResult("Number of sequences in ingroup", pscIn->getNumberOfSequences()); ApplicationTools::displayResult("Number of sequences in outgroup", pscOut.get() ? pscOut->getNumberOfSequences() : 0); // Shall we estimate some parameters first? bool estimateTsTv = ApplicationTools::getBooleanParameter("estimate.kappa", bpppopstats.getParams(), false, "", false, 1); double kappa = 1; double omega = -1; bool estimateAncestor = ApplicationTools::getBooleanParameter("estimate.ancestor", bpppopstats.getParams(), false, "", false, 1); if (estimateAncestor & ! pscOut) throw Exception("Error: an outgroup sequence is needed for estimating ancestral states."); bool fitModel = estimateTsTv || estimateAncestor; // Fit a model for later use: unique_ptr tree; unique_ptr model; unique_ptr rDist; DRTreeLikelihood* treeLik = nullptr; unique_ptr ancestralSequence; if (fitModel) { // Get the alignment: bool sampleIngroup = ApplicationTools::getBooleanParameter("estimate.sample_ingroup", bpppopstats.getParams(), true); size_t sampleIngroupSize = 0; if (sampleIngroup) { sampleIngroupSize = ApplicationTools::getParameter("estimate.sample_ingroup.size", bpppopstats.getParams(), 10); if (sampleIngroupSize > pscIn->getNumberOfSequences()) { ApplicationTools::displayWarning("Sample size higher than number of sequence. No sampling performed."); sampleIngroup = false; } } unique_ptr aln; if (sampleIngroup) { ApplicationTools::displayResult("Nb of ingroup sequences for model fitting", sampleIngroupSize); aln.reset(new AlignedSequenceContainer(pscIn->getAlphabet())); vector selection(sampleIngroupSize); RandomTools::getSample(pscIn->getSequencesNames(), selection, false); SequenceContainerTools::getSelectedSequences(*pscIn, selection ,*aln); } else { aln.reset(new AlignedSequenceContainer(*pscIn)); } if (pscOut) { aln->addSequence(pscOut->getSequence(0)); //As for now, we only consider one sequence as outgroup, the first one. } // Get a tree: string treeOpt = ApplicationTools::getStringParameter("input.tree.method", bpppopstats.getParams(), "bionj", ""); if (codonAlphabet) { unique_ptr freqSet(new FixedCodonFrequenciesSet(gCode.get())); model.reset(new YN98(gCode.get(), freqSet.release())); } else { model.reset(new K80(&AlphabetTools::DNA_ALPHABET)); } //Note: proteins not supported! rDist.reset(new ConstantRateDistribution()); if (treeOpt == "user") { tree.reset(PhylogeneticsApplicationTools::getTree(bpppopstats.getParams())); } else if (treeOpt == "bionj") { ApplicationTools::displayTask("Estimating distance matrix", true); //DistanceEstimation distEstimation(model->clone(), rDist->clone(), aln.get(), 1, false); //distEstimation.computeMatrix(); //unique_ptr matrix(distEstimation.getMatrix()); unique_ptr matrix(SiteContainerTools::computeSimilarityMatrix(*aln, true, SiteContainerTools::SIMILARITY_NOGAP, true)); ApplicationTools::displayTaskDone(); ApplicationTools::displayTask("Computing BioNJ tree", true); BioNJ bionj(false, true); bionj.setDistanceMatrix(*matrix); bionj.computeTree(); ApplicationTools::displayTaskDone(); tree.reset(bionj.getTree()); } else { throw Exception("Invalid input.tree.method. Should be either 'user' or 'bionj'."); } // Create a likelihood object: treeLik = new DRHomogeneousTreeLikelihood(*tree, *aln, model.get(), rDist.get()); treeLik->initialize(); if (std::isinf(treeLik->getValue())) throw Exception("Error: null likelihood. Possible cause: stop codon or numerical underflow (too many sequences)."); // Optimize parameters: treeLik = dynamic_cast(PhylogeneticsApplicationTools::optimizeParameters(treeLik, treeLik->getParameters(), bpppopstats.getParams(), "", true, true, 2)); // Get kappa: if (estimateTsTv) { kappa = model->getParameter("kappa").getValue(); ApplicationTools::displayResult("Transition / transversions ratio", kappa); } if (estimateAncestor) { MarginalAncestralStateReconstruction asr(treeLik); int outgroupId = tree->getLeafId(pscOut->getSequence(0).getName()); ancestralSequence.reset(asr.getAncestralSequenceForNode(tree->getFatherId(outgroupId))); } if (codonAlphabet) { omega = model->getParameter("omega").getValue(); } } if (treeLik) delete treeLik; //Not needed anymore. // +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ // Compute statistics vector actions = ApplicationTools::getVectorParameter("pop.stats", bpppopstats.getParams(), ',', "", "", false, 1); for (size_t a = 0; a < actions.size(); a++) { string cmdName; map cmdArgs; KeyvalTools::parseProcedure(actions[a], cmdName, cmdArgs); toolCounter[cmdName]++; // +-------------------+ // | Frequencies | // +-------------------+ if (cmdName == "SiteFrequencies") { unsigned int s = SequenceStatistics::numberOfPolymorphicSites(*pscIn); ApplicationTools::displayResult("Number of segregating sites:", s); unsigned int nsg = SequenceStatistics::numberOfSingletons(*pscIn); ApplicationTools::displayResult("Number of singletons:", nsg); //Print to logfile: if (logFile != "none") { *cLog << "# Site frequencies" << endl; *cLog << "NbSegSites" << (toolCounter[cmdName] > 1 ? TextTools::toString(toolCounter[cmdName]) : "") << " = " << s << endl; *cLog << "NbSingl" << (toolCounter[cmdName] > 1 ? TextTools::toString(toolCounter[cmdName]) : "") << " = " << nsg << endl; } } // +-------------------+ // | Watterson's theta | // +-------------------+ else if (cmdName == "Watterson75") { double thetaW75 = SequenceStatistics::watterson75(*pscIn, true, true, true); ApplicationTools::displayResult("Watterson's (1975) theta:", thetaW75); //Print to logfile: if (logFile != "none") { *cLog << "# Watterson's (1975) theta" << endl; *cLog << "thetaW75" << (toolCounter[cmdName] > 1 ? TextTools::toString(toolCounter[cmdName]) : "") << " = " << thetaW75 << endl; } } // +-------------+ // | Tajima's pi | // +-------------+ else if (cmdName == "Tajima83") { double piT83 = SequenceStatistics::tajima83(*pscIn, true, true, true); ApplicationTools::displayResult("Tajima's (1983) pi:", piT83); //Print to logfile: if (logFile != "none") { *cLog << "# Tajima's (1983) pi" << endl; *cLog << "piT83" << (toolCounter[cmdName] > 1 ? TextTools::toString(toolCounter[cmdName]) : "") << " = " << piT83 << endl; } } // +------------+ // | Tajima's D | // +------------+ else if (cmdName == "TajimaD") { string positions = ApplicationTools::getStringParameter("positions", cmdArgs, "all", "", false, 1); shared_ptr pscTmp; if ((positions == "synonymous" || positions == "non-synonymous") && !codonAlphabet) throw Exception("Error: synonymous and non-synonymous positions can only be defined with a codon alphabet."); if (positions == "synonymous") { pscTmp.reset(PolymorphismSequenceContainerTools::getSynonymousSites(*pscIn, *gCode)); } else if (positions == "non-synonymous") { pscTmp.reset(PolymorphismSequenceContainerTools::getNonSynonymousSites(*pscIn, *gCode)); } else if (positions == "all") { pscTmp = pscIn; } else throw Exception("Unrecognized option for argument 'positions': " + positions); if (SequenceStatistics::numberOfPolymorphicSites(*pscTmp) > 0) { double tajimaD = SequenceStatistics::tajimaDss(*pscTmp, true, true); ApplicationTools::displayResult("Tajima's (1989) D:", tajimaD); //Print to logfile: if (logFile != "none") { *cLog << "# Tajima's (1989) D (" << positions << " sites)" << endl; *cLog << "tajD" << (toolCounter[cmdName] > 1 ? TextTools::toString(toolCounter[cmdName]) : "") << " = " << tajimaD << endl; } } else { ApplicationTools::displayResult("Tajima's (1989) D:", "NA (0 polymorphic sites)"); if (logFile != "none") { *cLog << "# Tajima's (1989) D (" << positions << " sites)" << endl; *cLog << "tajD" << (toolCounter[cmdName] > 1 ? TextTools::toString(toolCounter[cmdName]) : "") << " = NA" << endl; } } } // +-----------+ // | FuAndLiD* | // +-----------+ else if (cmdName == "FuAndLiDStar") { bool useTotMut = ApplicationTools::getBooleanParameter("tot_mut", cmdArgs, true, "", false, 1); double flDstar = SequenceStatistics::fuLiDStar(*pscIn, !useTotMut); ApplicationTools::displayResult("Fu and Li's (1993) D*:", flDstar); ApplicationTools::displayResult(" computed using", (useTotMut ? "total number of mutations" : "number of segregating sites")); //Print to logfile: if (logFile != "none") { *cLog << "# Fu and Li's (1993) D*" << endl; if (useTotMut) *cLog << "fuLiDstarTotMut" << (toolCounter[cmdName] > 1 ? TextTools::toString(toolCounter[cmdName]) : "") << " = " << flDstar << endl; else *cLog << "fuLiDstarSegSit" << (toolCounter[cmdName] > 1 ? TextTools::toString(toolCounter[cmdName]) : "") << " = " << flDstar << endl; } } // +-----------+ // | FuAndLiF* | // +-----------+ else if (cmdName == "FuAndLiFStar") { bool useTotMut = ApplicationTools::getBooleanParameter("tot_mut", cmdArgs, true, "", false, 1); double flFstar = SequenceStatistics::fuLiFStar(*pscIn, !useTotMut); ApplicationTools::displayResult("Fu and Li (1993)'s F*:", flFstar); ApplicationTools::displayResult(" computed using", (useTotMut ? "total number of mutations" : "number of segregating sites")); //Print to logfile: if (logFile != "none") { *cLog << "# Fu and Li's (1993) F*" << endl; if (useTotMut) *cLog << "fuLiFstarTotMut" << (toolCounter[cmdName] > 1 ? TextTools::toString(toolCounter[cmdName]) : "") << " = " << flFstar << endl; else *cLog << "fuLiFstarSegSit" << (toolCounter[cmdName] > 1 ? TextTools::toString(toolCounter[cmdName]) : "") << " = " << flFstar << endl; } } // +-----------+ // | PiN / PiS | // +-----------+ else if (cmdName == "PiN_PiS") { if (!codonAlphabet) { throw Exception("PiN_PiS can only be used with a codon alignment. Check the input alphabet!"); } double piS = SequenceStatistics::piSynonymous(*pscIn, *gCode); double piN = SequenceStatistics::piNonSynonymous(*pscIn, *gCode); double nbS = SequenceStatistics::meanNumberOfSynonymousSites(*pscIn, *gCode, kappa); double nbN = SequenceStatistics::meanNumberOfNonSynonymousSites(*pscIn, *gCode, kappa); double r = (piN / nbN) / (piS / nbS); ApplicationTools::displayResult("PiN:", piN); ApplicationTools::displayResult("PiS:", piS); ApplicationTools::displayResult("#N:", nbN); ApplicationTools::displayResult("#S:", nbS); ApplicationTools::displayResult("PiN / PiS (corrected for #N and #S):", r); if (fitModel) { ApplicationTools::displayResult("Omega (YN98 model):", omega); } if (logFile != "none") { *cLog << "# PiN and PiS" << endl; *cLog << "PiN" << (toolCounter[cmdName] > 1 ? TextTools::toString(toolCounter[cmdName]) : "") << " = " << piN << endl; *cLog << "PiS" << (toolCounter[cmdName] > 1 ? TextTools::toString(toolCounter[cmdName]) : "") << " = " << piS << endl; *cLog << "NbN" << (toolCounter[cmdName] > 1 ? TextTools::toString(toolCounter[cmdName]) : "") << " = " << nbN << endl; *cLog << "NbS" << (toolCounter[cmdName] > 1 ? TextTools::toString(toolCounter[cmdName]) : "") << " = " << nbS << endl; if (fitModel) { *cLog << "Omega" << (toolCounter[cmdName] > 1 ? TextTools::toString(toolCounter[cmdName]) : "") << " = " << omega << endl; } } } // +---------+ // | dN / dS | // +---------+ else if (cmdName == "dN_dS") { if (!codonAlphabet) { throw Exception("dN_dS can only be used with a codon alignment. Check the input alphabet!"); } //Get consensus sequences: unique_ptr alnIn(pscIn->toSiteContainer()); unique_ptr alnOut(pscOut->toSiteContainer()); unique_ptr consensusIn(SiteContainerTools::getConsensus(*alnIn, "consIn", true, false)); unique_ptr consensusOut(SiteContainerTools::getConsensus(*alnOut, "consOut", true, false)); unique_ptr alnCons(new AlignedSequenceContainer(codonAlphabet)); alnCons->addSequence(*consensusIn); alnCons->addSequence(*consensusOut); unique_ptr freqSetDiv(new FixedCodonFrequenciesSet(gCode.get())); YN98* modelDiv = new YN98(gCode.get(), freqSetDiv.release()); DiscreteDistribution* rDistDiv = new ConstantRateDistribution(); DistanceEstimation distEstimation(modelDiv, rDistDiv, alnCons.get(), 0, false); distEstimation.setAdditionalParameters(modelDiv->getIndependentParameters()); distEstimation.computeMatrix(); unique_ptr matrix(distEstimation.getMatrix()); ApplicationTools::displayResult("Yang and Nielsen's Omega (dN/dS):", modelDiv->getParameter("omega").getValue()); ApplicationTools::displayResult("Yang and Nielsen's Kappa:", modelDiv->getParameter("kappa").getValue()); ApplicationTools::displayResult("Yang and Nielsen's Distance:", (*matrix)(1,0)); if (logFile != "none") { *cLog << "# dN and dS (Yang and Nielsen's 1998 substitution model)" << endl; *cLog << "OmegaDiv" << (toolCounter[cmdName] > 1 ? TextTools::toString(toolCounter[cmdName]) : "") << " = " << modelDiv->getParameter("omega").getValue() << endl; *cLog << "KappaDiv" << (toolCounter[cmdName] > 1 ? TextTools::toString(toolCounter[cmdName]) : "") << " = " << modelDiv->getParameter("kappa").getValue() << endl; *cLog << "DistanceDiv" << (toolCounter[cmdName] > 1 ? TextTools::toString(toolCounter[cmdName]) : "") << " = " << (*matrix)(1,0) << endl; } } // +---------+ // | MK test | // +---------+ else if (cmdName == "MKT") { if (!codonAlphabet) { throw Exception("MacDonald-Kreitman test can only be performed on a codon alignment. Check the input alphabet!"); } if (!pscOut) { throw Exception("MacDonald-Kreitman test requires at least one outgroup sequence."); } vector mktable = SequenceStatistics::mkTable(*pscIn, *pscOut, *gCode); ApplicationTools::displayResult("MK table, Pa:", mktable[0]); ApplicationTools::displayResult("MK table, Ps:", mktable[1]); ApplicationTools::displayResult("MK table, Da:", mktable[2]); ApplicationTools::displayResult("MK table, Ds:", mktable[3]); if (logFile != "none") { *cLog << "# MK table" << endl; *cLog << "# Pa Ps Da Ds" << endl; *cLog << "MKtable" << (toolCounter[cmdName] > 1 ? TextTools::toString(toolCounter[cmdName]) : "") << " = " << mktable[0] << " " << mktable[1] << " " << mktable[2] << " " << mktable[3] << endl; } } // +-----------------------+ // | Codon site statistics | // +-----------------------+ else if (cmdName == "CodonSiteStatistics") { if (!codonAlphabet) { throw Exception("CodonSiteStatstics can only be used with a codon alignment. Check the input alphabet!"); } string path = ApplicationTools::getAFilePath("output.file", cmdArgs, true, false); if (path == "none") throw Exception("You must specify an ouptut file for CodonSiteStatistics"); ApplicationTools::displayResult("Site statistics output to:", path); ofstream out(path.c_str(), ios::out); out << "Site\tMissingDataFrequency\tNbAlleles\tMinorAlleleFrequency\tMajorAlleleFrequency\tMinorAllele\tMajorAllele"; out << "\tMeanNumberSynPos\tIsSynPoly\tIs4Degenerated\tPiN\tPiS"; bool outgroup = (pscOut && pscOut->getNumberOfSequences() == 1); if (outgroup) { out << "\tOutgroupAllele"; } if (estimateAncestor) { out << "\tAncestralAllele"; } if (outgroup) { out << "\tMeanNumberSynPosDiv\tdN\tdS"; } out << endl; unique_ptr sites(pscIn->toSiteContainer()); for (size_t i = 0; i < sites->getNumberOfSites(); ++i) { const Site& site = sites->getSite(i); map counts; SymbolListTools::getCounts(site, counts); size_t minFreq = site.size() + 1; size_t maxFreq = 0; int minState = -1; int maxState = -1; size_t nbAlleles = 0; size_t nbMissing = 0; for (map::iterator it = counts.begin(); it != counts.end(); it++) { if (!alphabet->isUnresolved(it->first) && !alphabet->isGap(it->first)) { nbAlleles++; if (it->second != 0) { if (it->second < minFreq) { minFreq = it->second; minState = it->first; } if (it->second > maxFreq) { maxFreq = it->second; maxState = it->first; } } } else { nbMissing += it->second; } } out << site.getPosition() << "\t"; out << nbMissing << "\t"; out << nbAlleles << "\t"; out << minFreq << "\t"; out << maxFreq << "\t"; out << alphabet->intToChar(minState) << "\t"; out << alphabet->intToChar(maxState) << "\t"; if (estimateAncestor) { out << CodonSiteTools::numberOfSynonymousPositions(ancestralSequence->getValue(i), *gCode, kappa) << "\t"; } else { out << CodonSiteTools::meanNumberOfSynonymousPositions(site, *gCode, kappa) << "\t"; } out << CodonSiteTools::isSynonymousPolymorphic(site, *gCode) << "\t"; out << CodonSiteTools::isFourFoldDegenerated(site, *gCode) << "\t"; out << CodonSiteTools::piNonSynonymous(site, *gCode) << "\t"; out << CodonSiteTools::piSynonymous(site, *gCode); if (outgroup) { out << "\t" << pscOut->getSequence(0).getChar(i); } if (estimateAncestor) { out << "\t" << ancestralSequence->getChar(i); } if (outgroup) { //Add divergence int outgroupState = pscOut->getSequence(0)[i]; if (codonAlphabet->isUnresolved(outgroupState) || codonAlphabet->isGap(outgroupState)) { out << "\tNA\tNA\tNA"; } else { //Average over outgroup (Note: minState and maxState are identical in this case) out << "\t" << (CodonSiteTools::numberOfSynonymousPositions(outgroupState, *gCode, kappa) + CodonSiteTools::numberOfSynonymousPositions(minState, *gCode, kappa)) / 2.; if (nbAlleles == 1) { //Compare with outgroup: if (site[0] == outgroupState) { out << "\t0\t0"; } else { //This is a real substitution: double nt = static_cast(CodonSiteTools::numberOfDifferences(outgroupState, minState, *codonAlphabet)); double ns = CodonSiteTools::numberOfSynonymousDifferences(outgroupState, minState, *gCode); out << "\t" << (nt - ns) << "\t" << ns; } } else { //Site is polymorphic, this is not a substitution out << "\t0\t0"; } } } out << endl; } } else throw Exception("Unknown operation " + cmdName + "."); } // We're done! bpppopstats.done(); } catch (exception& e) { if (logFile != "none") *cLog << "# Error: " << e.what() << endl; cout << e.what() << endl; return 1; } return 0; } bppsuite-2.4.1/bppSuite/bppReRoot.cpp000066400000000000000000000261211333524216000175650ustar00rootroot00000000000000// // File: bppReRoot.cpp // Created by: Celine Scornavacca // Created on: Jan Tue 15 18:15 2008 // /* Copyright or © or Copr. Bio++ Development Team This software is a computer program whose purpose is to estimate phylogenies and evolutionary parameters from a dataset according to the maximum likelihood principle. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. */ // From the STL: #include using namespace std; // From bpp-core: #include #include #include #include #include #include #include // From bpp-phyl: #include #include #include #include #include #include using namespace bpp; typedef TreeTemplate MyTree; void help() { (*ApplicationTools::message << "bppreroot parameter1_name=parameter1_value").endLine(); (*ApplicationTools::message << " parameter2_name=parameter2_value ... param=option_file").endLine(); (*ApplicationTools::message).endLine(); (*ApplicationTools::message << " Refer to the Bio++ Program Suite Manual for a list of available options.").endLine(); } int main(int args, char ** argv) { cout << "******************************************************************" << endl; cout << "* Bio++ ReRoot, version " << BPP_VERSION << " *" << endl; cout << "* Author: C. Scornavacca Created 15/01/08 *" << endl; cout << "* Last Modif. " << BPP_REL_DATE << " *" << endl; cout << "******************************************************************" << endl; cout << endl; if(args == 1) { help(); return 0; } try { BppApplication bppreroot(args, argv, "BppReRoot"); bppreroot.startTimer(); Newick newick; string listPath = ApplicationTools::getAFilePath("input.list.file", bppreroot.getParams()); ApplicationTools::displayResult("Input list file", listPath); if(listPath == "none") throw Exception("You must provide an input tree list file."); string outgroupsPath = ApplicationTools::getAFilePath("outgroups.file", bppreroot.getParams()); ApplicationTools::displayResult("Outgroups file", outgroupsPath); if(outgroupsPath == "none") throw Exception("You must provide an outgroup list file."); string outputPath = ApplicationTools::getAFilePath("output.trees.file", bppreroot.getParams(), true, false); ApplicationTools::displayResult("Output file", outputPath); if(outputPath == "none") throw Exception("You must provide an output file."); bool printOption = ApplicationTools::getBooleanParameter("print.option", bppreroot.getParams(), false); bool tryAgain = ApplicationTools::getBooleanParameter("tryAgain.option", bppreroot.getParams(), true); vector tempTrees; vector trees; //ApplicationTools::displayResult("Number of trees found", TextTools::toString(trees.size())); const string path = outgroupsPath; ifstream file(path.c_str(), ios::in); string temp, description, taxon; vector < vector > levelOutgroup; //Reading outgroup levels while (!file.eof()) { vector tempTaxa; getline(file, temp, '\n'); StringTokenizer line = StringTokenizer(temp, " ,"); while (line.hasMoreToken()) { tempTaxa.push_back(line.nextToken()); } levelOutgroup.push_back(tempTaxa); } file.close(); const string path2 = listPath; ifstream treePath(path2.c_str(), ios::in); if (!treePath) { throw IOException ("Newick::read: failed to read from stream"); } string temp2, description2;// Initialization string::size_type index; int k = 0; while (!treePath.eof()) { k++; bool printOrNot =true; Tree * tempTree = NULL; getline(treePath, temp2, '\n'); // Copy current line in temporary string index = temp2.find(";"); if (temp2 != "") { if (index != string::npos) { description2 += temp2.substr(0, index + 1); tempTree = TreeTemplateTools::parenthesisToTree(description2); description2 = temp2.substr(index + 1); } else description2 += temp; MyTree* tree = dynamic_cast (tempTree); //ApplicationTools::displayGauge(tr, trees.size() - 1, '='); vector leavesTree; leavesTree = (*tree).getLeavesNames(); size_t numNodes = tree->getNumberOfNodes() - 1; size_t numNodeWithBranchLength = 0; vector nodes = tree->getNodes(); for (size_t i = 0; i < nodes.size(); i++) { if(nodes[i]->hasDistanceToFather()) numNodeWithBranchLength++; } if ((numNodes != numNodeWithBranchLength) && (numNodeWithBranchLength != 0))\ { cout << "Could not execute due to a source tree with missing branch lengths \n(reminder: a source tree must either have no branch length, either length for all branches\n"; exit(-1); } vector outGroup; bool found = false; bool analyseOutgroupLevel = true; for (size_t t = 0; t < levelOutgroup.size() && analyseOutgroupLevel; t++) { outGroup.clear(); vector::iterator Iterator; for(Iterator = levelOutgroup[t].begin(); Iterator != levelOutgroup[t].end(); Iterator++ ) { if(VectorTools::contains(leavesTree, *Iterator)) { outGroup.push_back(*Iterator); } } if(outGroup.size() > 0) { vector remainingTaxa; VectorTools::diff(leavesTree, outGroup, remainingTaxa); if(remainingTaxa.size() > 0) { tree->newOutGroup(tree->getNode(remainingTaxa[0])); Node * newRoot = tree->getNode(outGroup[0]); vector tempLeaves = TreeTemplateTools::getLeavesNames(* newRoot); while(newRoot->hasFather() && !(VectorTools::containsAll(tempLeaves, outGroup))) { newRoot = newRoot->getFather(); tempLeaves = TreeTemplateTools::getLeavesNames(* newRoot); } tempLeaves = TreeTemplateTools::getLeavesNames(* newRoot); std::sort(tempLeaves.begin(), tempLeaves.end()); if(tempLeaves.size() == outGroup.size()) { tree->newOutGroup(newRoot); found = true; analyseOutgroupLevel = false; } else { bool monophylOk = true; for (size_t f = 0; f < newRoot->getNumberOfSons() && monophylOk; f++) { tempLeaves = TreeTemplateTools::getLeavesNames(*newRoot->getSon(f)); vector diff; VectorTools::diff(outGroup, tempLeaves, diff); size_t difference = diff.size(); if (!( (difference == 0) || (difference == tempLeaves.size()) ) ) { //The proposed outgroup is not monophyletic. The analysis for this tree is interrupted //No more outgroup are analysed monophylOk = false; } } if (monophylOk) { tempLeaves = TreeTemplateTools::getLeavesNames(* newRoot); std::sort(tempLeaves.begin(), tempLeaves.end()); if (tempLeaves.size() != leavesTree.size()) { MyTree* low = new MyTree(TreeTemplateTools::cloneSubtree(* newRoot)); tree->newOutGroup(newRoot); Node* sonUpper; vector tempLeaves2 = TreeTemplateTools::getLeavesNames(* (tree->getRootNode())->getSon(0)); std::sort(tempLeaves2.begin(), tempLeaves2.end()); if((VectorTools::vectorIntersection(tempLeaves2,outGroup).size()) !=0) { sonUpper = (tree->getRootNode())->getSon(1); } else { sonUpper = (tree->getRootNode())->getSon(0); } int ident = TreeTools::getMaxId(*low, low->getRootId()); vector nodesTemp= TreeTemplateTools::getNodes( * sonUpper); for(size_t F = 0; F < nodesTemp.size(); F++) nodesTemp[F]->setId(ident + static_cast(F + 1)); low->getRootNode()->addSon(sonUpper); tree = low; } //A good outgroup was found found = true; analyseOutgroupLevel = false; } } } if(!tryAgain) analyseOutgroupLevel = false; } } if (!found) { if(!printOption) printOrNot = false; else printOrNot = true; cout << "Sorry but I can't root your tree " << k << " ; or none of the taxa in your list is present in the tree or the outgroup is not monophyletic!\n"; } else { printOrNot = (true); tree->resetNodesId(); } if (printOrNot) { if(k == 1) newick.write(* tree, outputPath, true); else newick.write(* tree, outputPath, false); } delete tree; } } ApplicationTools::displayTaskDone(); //Write rooted trees: for (size_t i = 0; i < trees.size(); i++) delete trees[i]; bppreroot.done(); } catch(exception & e) { cout << e.what() << endl; return 1; } return 0; }; bppsuite-2.4.1/bppSuite/bppSeqGen.cpp000066400000000000000000000643211333524216000175410ustar00rootroot00000000000000// // File: bppSeqGen.cpp // Created by: Julien Dutheil // Created on: Oct Mon 24 18:50 2005 // /* Copyright or � or Copr. Bio++ Development Team This software is a computer program whose purpose is to simulate sequence data according to a phylogenetic tree and an evolutionary model. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. */ // From the STL: #include #include #include using namespace std; // From bpp-core: #include #include #include #include #include #include #include #include #include #include #include // From bpp-seq: #include #include #include #include #include // From bpp-phyl: #include #include #include #include #include #include #include #include using namespace bpp; /** * @brief Read trees from an input file, with segment annotations. Hudson's MS format. */ void readTreesMs(ifstream& file, vector& trees, vector& pos, unsigned int totPos) { string line = ""; unsigned int segsize; unsigned int previous = 0; string::size_type index; pos.push_back(0); string newickStr; bool start = false; while (!file.eof() && !start) { line = TextTools::removeSurroundingWhiteSpaces(FileTools::getNextLine(file)); start = (line == "//"); } ApplicationTools::displayTask("Reading tress for each partition"); while (!file.eof()) { line = TextTools::removeSurroundingWhiteSpaces(FileTools::getNextLine(file)); ApplicationTools::displayGauge(previous, totPos, '='); if (line.size() == 0 || (line.substr(0, 1) != "[" && line.substr(0, 1) != "(" )) continue; if (line.substr(0, 1) == "(") { //This is a single tree, no recombination event TreeTemplate* t = TreeTemplateTools::parenthesisToTree(line, true, TreeTools::BOOTSTRAP, false, false); trees.push_back(t); pos.push_back(1); return; } index = line.find("]"); if (index == string::npos) throw Exception("Error when parsing tree file: no valid position."); segsize = TextTools::to(line.substr(1, index - 1)); newickStr = line.substr(index + 1); TreeTemplate* t = TreeTemplateTools::parenthesisToTree(newickStr, true, TreeTools::BOOTSTRAP, false, false); if (trees.size() > 0) { //Check leave names: if (!VectorTools::haveSameElements(t->getLeavesNames(), trees[trees.size()-1]->getLeavesNames())) throw Exception("Error: all trees must have the same leaf names."); } trees.push_back(t); previous += segsize; pos.push_back(static_cast(previous) / static_cast(totPos)); //Convert to relative positions } ApplicationTools::displayGauge(totPos, totPos, '='); ApplicationTools::displayTaskDone(); } /** * @brief Read trees from an input file, with segment annotations. Mailund's CoaSim format. */ void readTreesCoaSim(ifstream& file, vector& trees, vector& pos) { string line = ""; double begin, end; string::size_type index1, index2, index3; double previousPos = 0; pos.push_back(0); string newickStr; while (!file.eof()) { string tmp = TextTools::removeSurroundingWhiteSpaces(FileTools::getNextLine(file)); if (tmp.size() == 0 || tmp.substr(0, 1) == "#") continue; line += tmp; index1 = line.find_first_of(" \t"); if (index1 == string::npos) throw Exception("Error when parsing tree file: no begining position."); index2 = line.find_first_of(" \t", index1 + 1); if (index2 == string::npos) throw Exception("Error when parsing tree file: no ending position."); begin = TextTools::toDouble(line.substr(0, index1)); end = TextTools::toDouble(line.substr(index1 + 1, index2 - index1 - 1)); index3 = line.find_first_of(";", index2 + 1); while (index3 == string::npos) { if (file.eof()) throw Exception("Error when parsing tree file: incomplete tree."); line += FileTools::getNextLine(file); index3 = line.find_first_of(";", index3); } newickStr = line.substr(index2 + 1, index3 - index2); TreeTemplate* t = TreeTemplateTools::parenthesisToTree(newickStr, true, TreeTools::BOOTSTRAP, false, false); if (trees.size() > 0) { //Check leave names: if (!VectorTools::haveSameElements(t->getLeavesNames(), trees[trees.size()-1]->getLeavesNames())) throw Exception("Error: all trees must have the same leaf names."); } trees.push_back(t); if(begin != previousPos) throw Exception("Error when parsing tree file: segments do not match: " + TextTools::toString(begin) + " against " + TextTools::toString(previousPos) + "."); pos.push_back(end); previousPos = end; line = line.substr(index3 + 1); } } void help() { (*ApplicationTools::message << "__________________________________________________________________________").endLine(); (*ApplicationTools::message << "bppseqgen parameter1_name=parameter1_value").endLine(); (*ApplicationTools::message << " parameter2_name=parameter2_value ... param=option_file").endLine(); (*ApplicationTools::message).endLine(); (*ApplicationTools::message << " Refer to the Bio++ Program Suite Manual for a list of available options.").endLine(); (*ApplicationTools::message << "__________________________________________________________________________").endLine(); } int main(int args, char ** argv) { cout << "******************************************************************" << endl; cout << "* Bio++ Sequence Generator, version " << BPP_VERSION << " *" << endl; cout << "* *" << endl; cout << "* Authors: J. Dutheil *" << endl; cout << "* B. Boussau Last Modif. " << BPP_REL_DATE << " *" << endl; cout << "* L. Gueguen *" << endl; cout << "* M. Groussin *" << endl; cout << "******************************************************************" << endl; cout << endl; if(args == 1) { help(); return 0; } try { BppApplication bppseqgen(args, argv, "BppSeqGen"); bppseqgen.startTimer(); Alphabet* alphabet = SequenceApplicationTools::getAlphabet(bppseqgen.getParams(), "", false); unique_ptr gCode; CodonAlphabet* codonAlphabet = dynamic_cast(alphabet); if (codonAlphabet) { string codeDesc = ApplicationTools::getStringParameter("genetic_code", bppseqgen.getParams(), "Standard", "", true, true); ApplicationTools::displayResult("Genetic Code", codeDesc); gCode.reset(SequenceApplicationTools::getGeneticCode(codonAlphabet->getNucleicAlphabet(), codeDesc)); } /**************************/ /* Trees */ /**************************/ vector trees; vector positions; string inputTrees = ApplicationTools::getStringParameter("input.tree.method", bppseqgen.getParams(), "single", "", true, false); string itName; map itArgs; KeyvalTools::parseProcedure(inputTrees, itName, itArgs); if (itName == "single") { trees.push_back(PhylogeneticsApplicationTools::getTree(bppseqgen.getParams())); positions.push_back(0); positions.push_back(1); ApplicationTools::displayResult("Number of leaves", TextTools::toString(trees[0]->getNumberOfLeaves())); string treeWIdPath = ApplicationTools::getAFilePath("output.tree_ids.file", bppseqgen.getParams(), false, false); if (treeWIdPath != "none") { TreeTemplate ttree(*trees[0]); vector nodes = ttree.getNodes(); for (size_t i = 0; i < nodes.size(); i++) { if (nodes[i]->isLeaf()) nodes[i]->setName(TextTools::toString(nodes[i]->getId()) + "_" + nodes[i]->getName()); else nodes[i]->setBranchProperty("NodeId", BppString(TextTools::toString(nodes[i]->getId()))); } Newick treeWriter; treeWriter.enableExtendedBootstrapProperty("NodeId"); ApplicationTools::displayResult("Writing tagged tree to", treeWIdPath); treeWriter.write(ttree, treeWIdPath); delete trees[0]; cout << "BppSegGen's done." << endl; exit(0); } } else if (itName == "multiple") { throw Exception("'multiple' option deprecated, use 'coasim' instead."); } else if (itName == "CoaSim") { string treesPath = ApplicationTools::getAFilePath("input.tree.file", bppseqgen.getParams(), false, true); ApplicationTools::displayResult("Trees file", treesPath); ifstream treesFile(treesPath.c_str(), ios::in); readTreesCoaSim(treesFile, trees, positions); } else if (itName == "MS") { string treesPath = ApplicationTools::getAFilePath("input.tree.file", bppseqgen.getParams(), false, true); unsigned int totPos = ApplicationTools::getParameter("number_of_sites", itArgs, 100); ApplicationTools::displayResult("Total # sites in ARG", totPos); ApplicationTools::displayResult("Trees file", treesPath); ifstream treesFile(treesPath.c_str(), ios::in); readTreesMs(treesFile, trees, positions, totPos); } else throw Exception("Unknown input.tree.method option: " + inputTrees); // Scaling of trees: double scale = ApplicationTools::getDoubleParameter("input.tree.scale", bppseqgen.getParams(), 1, "", false, false); if (scale != 1) { ApplicationTools::displayResult("Trees are scaled by", scale); for (Tree* tree : trees) { tree -> scaleTree(scale); } } /**********************************/ /* Models */ /**********************************/ string nhOpt = ApplicationTools::getStringParameter("nonhomogeneous", bppseqgen.getParams(), "no", "", true, false); ApplicationTools::displayResult("Heterogeneous model", nhOpt); SubstitutionModelSet* modelSet = 0; //Homogeneous case: if (nhOpt == "no") { TransitionModel* model = PhylogeneticsApplicationTools::getTransitionModel(alphabet, gCode.get(), 0, bppseqgen.getParams()); FrequenciesSet* fSet = new FixedFrequenciesSet(model->getStateMap().clone(), model->getFrequencies()); modelSet = SubstitutionModelSetTools::createHomogeneousModelSet(model, fSet, trees[0]); } //Galtier-Gouy case: else if (nhOpt == "one_per_branch") { if(itName == "MS" || itName == "CoaSim") throw Exception("Multiple input trees cannot be used with non-homogeneous simulations."); TransitionModel* model = 0; string modelName = ApplicationTools::getStringParameter("model", bppseqgen.getParams(), ""); if (!TextTools::hasSubstring(modelName,"COaLA")) model = PhylogeneticsApplicationTools::getTransitionModel(alphabet, gCode.get(), 0, bppseqgen.getParams()); else { //COaLA model VectorSiteContainer* allSitesAln = 0; allSitesAln = SequenceApplicationTools::getSiteContainer(alphabet, bppseqgen.getParams()); model = PhylogeneticsApplicationTools::getTransitionModel(alphabet, gCode.get(), allSitesAln, bppseqgen.getParams()); } vector globalParameters = ApplicationTools::getVectorParameter("nonhomogeneous_one_per_branch.shared_parameters", bppseqgen.getParams(), ',', ""); vector rateFreqs; if (model->getNumberOfStates() != alphabet->getSize()) { //Markov-Modulated Markov Model... unsigned int n = static_cast(model->getNumberOfStates() / alphabet->getSize()); rateFreqs = vector(n, 1./static_cast(n)); // Equal rates assumed for now, may be changed later (actually, in the most general case, // we should assume a rate distribution for the root also!!! } std::map aliasFreqNames; FrequenciesSet* rootFreqs = PhylogeneticsApplicationTools::getRootFrequenciesSet(alphabet, gCode.get(), 0, bppseqgen.getParams(), aliasFreqNames, rateFreqs); string freqDescription = ApplicationTools::getStringParameter("nonhomogeneous.root_freq", bppseqgen.getParams(), "Full(init=observed)"); if (freqDescription.substr(0,10) == "MVAprotein") { dynamic_cast(rootFreqs)->setModelName("MVAprotein"); dynamic_cast(rootFreqs)->initSet(dynamic_cast(model)); } modelSet = SubstitutionModelSetTools::createNonHomogeneousModelSet(model, rootFreqs, trees[0], aliasFreqNames, globalParameters); } //General case: else if (nhOpt == "general") { if (itName == "MS" || itName == "CoaSim") throw Exception("Multiple input trees cannot be used with non-homogeneous simulations."); string modelName = ApplicationTools::getStringParameter("model1",bppseqgen.getParams(),""); if (!TextTools::hasSubstring(modelName,"COaLA")) modelSet = PhylogeneticsApplicationTools::getSubstitutionModelSet(alphabet, gCode.get(), 0, bppseqgen.getParams()); else { //COaLA model VectorSiteContainer* allSitesAln = 0; allSitesAln = SequenceApplicationTools::getSiteContainer(alphabet, bppseqgen.getParams()); modelSet = PhylogeneticsApplicationTools::getSubstitutionModelSet(alphabet, gCode.get(), allSitesAln, bppseqgen.getParams()); } } else throw Exception("Unknown non-homogeneous option: " + nhOpt); if (dynamic_cast(modelSet)) throw Exception("Non-homogeneous mixed substitution sequence generation not implemented, sorry!"); /*******************************************/ /* Starting sequence */ /*******************************************/ DiscreteDistribution* rDist = 0; NonHomogeneousSequenceSimulator* seqsim = 0; SiteContainer* sites = 0; size_t nbSites = 0; bool outputInternalSequences = ApplicationTools::getBooleanParameter("output.internal.sequences", bppseqgen.getParams(), false, "", true, 1); string infosFile = ApplicationTools::getAFilePath("input.infos", bppseqgen.getParams(), false, true); bool withStates = false; bool withRates = false; vector states; vector rates; if (infosFile != "none") { ApplicationTools::displayResult("Site information", infosFile); ifstream in(infosFile.c_str()); DataTable* infos = DataTable::read(in, "\t"); nbSites = infos->getNumberOfRows(); ApplicationTools::displayResult("Number of sites", TextTools::toString(nbSites)); string rateCol = ApplicationTools::getStringParameter("input.infos.rates", bppseqgen.getParams(), "pr", "", true, true); string stateCol = ApplicationTools::getStringParameter("input.infos.states", bppseqgen.getParams(), "none", "", true, true); withRates = rateCol != "none"; withStates = stateCol != "none"; if (withRates) { rDist = new ConstantRateDistribution(); rates.resize(nbSites); vector ratesStrings = infos->getColumn(rateCol); for (size_t i = 0; i < nbSites; i++) { rates[i] = TextTools::toDouble(ratesStrings[i]); } } if (withStates) { vector ancestralStates = infos->getColumn(stateCol); states.resize(nbSites); for (size_t i = 0; i < nbSites; i++) { int alphabetState = alphabet->charToInt(ancestralStates[i]); //If a generic character is provided, we pick one state randomly from the possible ones: if (alphabet->isUnresolved(alphabetState)) alphabetState = RandomTools::pickOne(alphabet->getAlias(alphabetState)); states[i] = RandomTools::pickOne(modelSet->getModelStates(alphabetState)); } string siteSet = ApplicationTools::getStringParameter("input.site.selection", bppseqgen.getParams(), "none", "", true, 1); if (siteSet != "none") { vector vSite; try { vector vSite1 = NumCalcApplicationTools::seqFromString(siteSet); for (size_t i = 0; i < vSite1.size(); ++i){ int x = (vSite1[i] >= 0 ? vSite1[i] : static_cast(nbSites) + vSite1[i]); if (x >= 0) vSite.push_back(static_cast(x)); else throw Exception("SequenceApplicationTools::getSiteContainer(). Incorrect negative index: " + TextTools::toString(x)); } } catch (Exception& e) { string seln; map selArgs; KeyvalTools::parseProcedure(siteSet, seln, selArgs); if (seln == "Sample") { size_t n = ApplicationTools::getParameter("n", selArgs, nbSites, "", true, 1); bool replace = ApplicationTools::getBooleanParameter("replace", selArgs, false, "", true, 1); vSite.resize(n); vector vPos; for (size_t p = 0; p < nbSites; ++p) vPos.push_back(p); RandomTools::getSample(vPos, vSite, replace); } } nbSites = vSite.size(); vector newStates(nbSites); vector newRates(nbSites); for (size_t ni = 0; ni < nbSites; ++ni) { newStates[ni] = states[vSite[ni]]; newRates[ni] = rates[vSite[ni]]; } states = newStates; rates = newRates; } } } else { try { VectorSiteContainer* allSeq = 0; allSeq = SequenceApplicationTools::getSiteContainer(alphabet, bppseqgen.getParams()); if (allSeq->getNumberOfSequences() > 0) { Sequence* pseq = SequenceTools::getSequenceWithCompleteSites(allSeq->getSequence(0)); nbSites = pseq->size(); states.resize(nbSites); withStates = true; for (size_t i = 0; i < nbSites; ++i) { states[i] = RandomTools::pickOne(modelSet->getModelStates((*pseq)[i])); } ApplicationTools::displayResult("Number of sites", TextTools::toString(nbSites)); delete pseq; } } catch (Exception& e) { } } if (rDist == 0) { if (modelSet->getNumberOfStates() > modelSet->getAlphabet()->getSize()) { //Markov-modulated Markov model! rDist = new ConstantRateDistribution(); } else { rDist = PhylogeneticsApplicationTools::getRateDistribution(bppseqgen.getParams()); } } if (nbSites == 0) nbSites = ApplicationTools::getParameter("number_of_sites", bppseqgen.getParams(), 100); /*******************/ /* Simulations */ /*******************/ if (withStates) { if (trees.size() == 1) { seqsim = new NonHomogeneousSequenceSimulator(modelSet, rDist, trees[0]); seqsim->outputInternalSequences(outputInternalSequences); ApplicationTools::displayTask("Perform simulations"); if (withRates) if (withStates) sites = SequenceSimulationTools::simulateSites(*seqsim, rates, states); else sites = SequenceSimulationTools::simulateSites(*seqsim, rates); else if (withStates){ sites = SequenceSimulationTools::simulateSites(*seqsim, states); } else throw Exception("Error! Info file should contain either site specific rates of ancestral states or both."); delete seqsim; } else { ApplicationTools::displayTask("Perform simulations", true); ApplicationTools::displayGauge(0, trees.size() - 1, '='); seqsim = new NonHomogeneousSequenceSimulator(modelSet, rDist, trees[0]); seqsim->outputInternalSequences(outputInternalSequences); ptrdiff_t previousPos = 0; ptrdiff_t currentPos = static_cast(round(positions[1]*static_cast(nbSites))); vector tmpRates; if (withRates) tmpRates = vector(rates.begin() + previousPos, rates.begin() + currentPos); vector tmpStates; if (withStates) tmpStates = vector(states.begin() + previousPos, states.begin() + currentPos); SequenceContainer* tmpCont1 = 0; if (withRates) if (withStates) tmpCont1 = SequenceSimulationTools::simulateSites(*seqsim, tmpRates, tmpStates); else tmpCont1 = SequenceSimulationTools::simulateSites(*seqsim, tmpRates); else if (withStates) tmpCont1 = SequenceSimulationTools::simulateSites(*seqsim, tmpStates); else throw Exception("Error! Info file should contain either site specific rates of ancestral states or both."); previousPos = currentPos; delete seqsim; for(size_t i = 1; i < trees.size(); i++) { ApplicationTools::displayGauge(i, trees.size() - 1, '='); seqsim = new NonHomogeneousSequenceSimulator(modelSet, rDist, trees[i]); seqsim->outputInternalSequences(outputInternalSequences); currentPos = static_cast(round(positions[i+1]) * static_cast(nbSites)); if (withRates) tmpRates = vector(rates.begin() + previousPos + 1, rates.begin() + currentPos); if (withStates) tmpStates = vector(states.begin() + previousPos + 1, states.begin() + currentPos); SequenceContainer* tmpCont2 = 0; if (withRates) if (withStates) tmpCont2 = SequenceSimulationTools::simulateSites(*seqsim, tmpRates, tmpStates); else tmpCont2 = SequenceSimulationTools::simulateSites(*seqsim, tmpRates); else if (withStates) tmpCont2 = SequenceSimulationTools::simulateSites(*seqsim, tmpStates); else throw Exception("Error! Info file should contain either site specific rates of ancestral states or both."); previousPos = currentPos; delete seqsim; VectorSequenceContainer* mergedCont = new VectorSequenceContainer(alphabet); SequenceContainerTools::merge(*tmpCont1, *tmpCont2, *mergedCont); delete tmpCont1; delete tmpCont2; tmpCont1 = mergedCont; } sites = new VectorSiteContainer(*tmpCont1); delete tmpCont1; } ApplicationTools::displayTaskDone(); } else { if (modelSet->getNumberOfStates() > modelSet->getAlphabet()->getSize()) { //Markov-modulated Markov model! rDist = new ConstantRateDistribution(); } else { rDist = PhylogeneticsApplicationTools::getRateDistribution(bppseqgen.getParams()); } if (trees.size() == 1) { seqsim = new NonHomogeneousSequenceSimulator(modelSet, rDist, trees[0]); seqsim->outputInternalSequences(outputInternalSequences); ApplicationTools::displayResult("Number of sites", TextTools::toString(nbSites)); ApplicationTools::displayTask("Perform simulations"); sites = seqsim->simulate(nbSites); ApplicationTools::displayTaskDone(); } else { ApplicationTools::displayTask("Perform simulations", true); ApplicationTools::displayGauge(0, trees.size() - 1, '='); seqsim = new NonHomogeneousSequenceSimulator(modelSet, rDist, trees[0]); seqsim->outputInternalSequences(outputInternalSequences); size_t previousPos = 0; size_t currentPos = static_cast(round(positions[1] * static_cast(nbSites))); SequenceContainer* tmpCont1 = seqsim->simulate(currentPos - previousPos); previousPos = currentPos; delete seqsim; for (size_t i = 1; i < trees.size(); i++) { ApplicationTools::displayGauge(i, trees.size() - 1, '='); seqsim = new NonHomogeneousSequenceSimulator(modelSet, rDist, trees[i]); seqsim->outputInternalSequences(outputInternalSequences); currentPos = static_cast(round(positions[i+1] * static_cast(nbSites))); SequenceContainer* tmpCont2 = seqsim->simulate(currentPos - previousPos); previousPos = currentPos; delete seqsim; VectorSequenceContainer* mergedCont = new VectorSequenceContainer(alphabet); SequenceContainerTools::merge(*tmpCont1, *tmpCont2, *mergedCont); delete tmpCont1; delete tmpCont2; tmpCont1 = mergedCont; } sites = new VectorSiteContainer(*tmpCont1); ApplicationTools::displayTaskDone(); delete tmpCont1; } } // Write to file: SequenceApplicationTools::writeAlignmentFile(*sites, bppseqgen.getParams()); delete alphabet; for (size_t i = 0; i < trees.size(); i++) delete trees[i]; delete rDist; bppseqgen.done(); } catch (exception& e) { cout << e.what() << endl; return 1; } return 0; } bppsuite-2.4.1/bppSuite/bppSeqMan.cpp000066400000000000000000000510431333524216000175400ustar00rootroot00000000000000// // File: bppSeqMan.cpp // Created by: Julien Dutheil // Created on: Oct Tue 02 9:00 2007 // /* Copyright or © or Copr. Bio++ Development Team This software is a computer program whose purpose is to simulate sequence data according to a phylogenetic tree and an evolutionary model. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. */ // From the STL: #include #include #include using namespace std; // From bpp-core: #include #include #include #include #include // From bpp-seq: #include #include #include #include #include #include #include #include #include //From bpp-phyl: #include #include using namespace bpp; void help() { (*ApplicationTools::message << "__________________________________________________________________________").endLine(); (*ApplicationTools::message << "bppseqman parameter1_name=parameter1_value").endLine(); (*ApplicationTools::message << " parameter2_name=parameter2_value ... param=option_file").endLine(); (*ApplicationTools::message).endLine(); (*ApplicationTools::message << " Refer to the Bio++ Program Suite Manual for a list of available options.").endLine(); (*ApplicationTools::message << "__________________________________________________________________________").endLine(); } int main(int args, char** argv) { cout << "******************************************************************" << endl; cout << "* Bio++ Sequence Manipulator, version " << BPP_VERSION << ". *" << endl; cout << "* Author: J. Dutheil Last Modif. " << BPP_REL_DATE << " *" << endl; cout << "******************************************************************" << endl; cout << endl; if (args == 1) { help(); return 0; } try { BppApplication bppseqman(args, argv, "BppSeqMan"); bppseqman.startTimer(); // Get alphabet Alphabet* alphabet = SequenceApplicationTools::getAlphabet(bppseqman.getParams(), "", false, true, true); unique_ptr gCode; CodonAlphabet* codonAlphabet = dynamic_cast(alphabet); // Get sequences: bool aligned = ApplicationTools::getBooleanParameter("input.alignment", bppseqman.getParams(), false, "", true, 1); OrderedSequenceContainer* sequences = 0; if (aligned) { VectorSiteContainer* allSites = SequenceApplicationTools::getSiteContainer(alphabet, bppseqman.getParams()); sequences = SequenceApplicationTools::getSitesToAnalyse(*allSites, bppseqman.getParams(), "", true, false); delete allSites; } else { SequenceContainer* tmp = SequenceApplicationTools::getSequenceContainer(alphabet, bppseqman.getParams(), "", true, true); sequences = new VectorSequenceContainer(*tmp); delete tmp; } ApplicationTools::displayResult("Number of sequences", sequences->getNumberOfSequences()); // Perform manipulations vector actions = ApplicationTools::getVectorParameter("sequence.manip", bppseqman.getParams(), ',', "", "", false, 1); for (size_t a = 0; a < actions.size(); a++) { string cmdName; map cmdArgs; KeyvalTools::parseProcedure(actions[a], cmdName, cmdArgs); ApplicationTools::displayResult("Performing action", cmdName); // +-----------------+ // | Complementation | // +-----------------+ if (cmdName == "Complement") { OrderedSequenceContainer* sc = 0; if (aligned) sc = new VectorSiteContainer(sequences->getAlphabet()); else sc = new VectorSequenceContainer(sequences->getAlphabet()); for (size_t i = 0; i < sequences->getNumberOfSequences(); i++) { Sequence* seq = SequenceTools::getComplement(sequences->getSequence(i)); sc->addSequence(*seq, false); delete seq; } delete sequences; sequences = sc; } // +------------------------+ // | (Reverse)Transcription | // +------------------------+ else if (cmdName == "Transcript") { if (sequences->getAlphabet()->getAlphabetType() == AlphabetTools::DNA_ALPHABET.getAlphabetType()) { OrderedSequenceContainer* sc = 0; if (aligned) sc = new VectorSiteContainer(&AlphabetTools::RNA_ALPHABET); else sc = new VectorSequenceContainer(&AlphabetTools::RNA_ALPHABET); for (unsigned int i = 0; i < sequences->getNumberOfSequences(); i++) { Sequence* seq = SequenceTools::transcript(sequences->getSequence(i)); sc->addSequence(*seq, false); delete seq; } delete sequences; sequences = sc; } else if (sequences->getAlphabet()->getAlphabetType() == AlphabetTools::RNA_ALPHABET.getAlphabetType()) { OrderedSequenceContainer* sc = 0; if (aligned) sc = new VectorSiteContainer(&AlphabetTools::DNA_ALPHABET); else sc = new VectorSequenceContainer(&AlphabetTools::DNA_ALPHABET); for (unsigned int i = 0; i < sequences->getNumberOfSequences(); i++) { Sequence* seq = SequenceTools::reverseTranscript(sequences->getSequence(i)); sc->addSequence(*seq, false); delete seq; } delete sequences; sequences = sc; } else throw Exception("Transcription error: input alphabet must be of type 'nucleic'."); } // +-------------------------------+ // | Switching nucleotide alphabet | // +-------------------------------+ else if (cmdName == "Switch") { const Alphabet* alpha = 0; if (sequences->getAlphabet()->getAlphabetType() == AlphabetTools::DNA_ALPHABET.getAlphabetType()) { alpha = &AlphabetTools::RNA_ALPHABET; } else if (sequences->getAlphabet()->getAlphabetType() == AlphabetTools::RNA_ALPHABET.getAlphabetType()) { alpha = &AlphabetTools::DNA_ALPHABET; } else throw Exception("Cannot switch alphabet type, alphabet is not of type 'nucleic'."); OrderedSequenceContainer* sc = 0; if (aligned) sc = new VectorSiteContainer(alpha); else sc = new VectorSequenceContainer(alpha); for (size_t i = 0; i < sequences->getNumberOfSequences(); i++) { const Sequence* old = &sequences->getSequence(i); vector content(old->size()); for (size_t j = 0; j < old->size(); ++j) content[j] = (*old)[j]; Sequence* seq = new BasicSequence(old->getName(), content, old->getComments(), alpha); sc->addSequence(*seq, false); delete seq; } delete sequences; sequences = sc; } // +-------------+ // | Translation | // +-------------+ else if (cmdName == "Translate") { if (!AlphabetTools::isCodonAlphabet(sequences->getAlphabet())) throw Exception("Error in translation: alphabet is not of type 'codon'."); if (cmdArgs["code"] != "") throw Exception("ERROR: 'code' argument is deprecated. The genetic code to use for translation is now set by the top-level argument 'genetic_code'."); if (!gCode.get()) { string codeDesc = ApplicationTools::getStringParameter("genetic_code", bppseqman.getParams(), "Standard", "", true, 1); ApplicationTools::displayResult("Genetic Code", codeDesc); gCode.reset(SequenceApplicationTools::getGeneticCode(codonAlphabet->getNucleicAlphabet(), codeDesc)); } OrderedSequenceContainer* sc = 0; if (aligned) sc = new VectorSiteContainer(&AlphabetTools::PROTEIN_ALPHABET); else sc = new VectorSequenceContainer(&AlphabetTools::PROTEIN_ALPHABET); for (size_t i = 0; i < sequences->getNumberOfSequences(); ++i) { Sequence* seq = gCode->translate(sequences->getSequence(i)); sc->addSequence(*seq, false); delete seq; } delete sequences; sequences = sc; } // +-------------+ // | Remove gaps | // +-------------+ else if (cmdName == "RemoveGaps") { VectorSequenceContainer* sc = new VectorSequenceContainer(sequences->getAlphabet()); for (size_t i = 0; i < sequences->getNumberOfSequences(); i++) { unique_ptr seq(sequences->getSequence(i).clone()); SequenceTools::removeGaps(*seq); sc->addSequence(*seq); } delete sequences; sequences = sc; aligned = false; } // +---------------------------+ // | Change gaps to unresolved | // +---------------------------+ else if (cmdName == "GapToUnknown") { OrderedSequenceContainer* sc = 0; if (aligned) sc = new VectorSiteContainer(sequences->getAlphabet()); else sc = new VectorSequenceContainer(sequences->getAlphabet()); for (size_t i = 0; i < sequences->getNumberOfSequences(); i++) { Sequence* seq = new BasicSequence(sequences->getSequence(i)); SymbolListTools::changeGapsToUnknownCharacters(*seq); sc->addSequence(*seq, false); delete seq; } delete sequences; sequences = sc; } // +---------------------------+ // | Change unresolved to gaps | // +---------------------------+ else if (cmdName == "UnknownToGap") { OrderedSequenceContainer* sc = 0; if (aligned) sc = new VectorSiteContainer(sequences->getAlphabet()); else sc = new VectorSequenceContainer(sequences->getAlphabet()); for (size_t i = 0; i < sequences->getNumberOfSequences(); i++) { Sequence* seq = new BasicSequence(sequences->getSequence(i)); SymbolListTools::changeUnresolvedCharactersToGaps(*seq); sc->addSequence(*seq, false); delete seq; } delete sequences; sequences = sc; } // +--------------+ // | Remove stops | // +--------------+ else if (cmdName == "RemoveStops") { if (!codonAlphabet) throw Exception("RemoveStops: requires a codon alphabet."); if (!gCode.get()) { string codeDesc = ApplicationTools::getStringParameter("genetic_code", bppseqman.getParams(), "Standard", "", true, 1); ApplicationTools::displayResult("Genetic Code", codeDesc); gCode.reset(SequenceApplicationTools::getGeneticCode(codonAlphabet->getNucleicAlphabet(), codeDesc)); } SiteContainer* sites = dynamic_cast(sequences); if (!sites) { VectorSequenceContainer* sc = new VectorSequenceContainer(sequences->getAlphabet()); for (size_t i = 0; i < sequences->getNumberOfSequences(); ++i) { unique_ptr seq(sequences->getSequence(i).clone()); SequenceTools::removeStops(*seq, *gCode); sc->addSequence(*seq); } delete sequences; sequences = sc; } else { VectorSiteContainer* sc = new VectorSiteContainer(sequences->getAlphabet()); for (size_t i = 0; i < sequences->getNumberOfSequences(); ++i) { unique_ptr seq(sequences->getSequence(i).clone()); SequenceTools::replaceStopsWithGaps(*seq, *gCode); sc->addSequence(*seq); } delete sequences; sequences = sc; } } // +--------------+ // | Remove stops | // +--------------+ else if (cmdName == "RemoveColumnsWithStops") { SiteContainer* sites = dynamic_cast(sequences); if (!sites) { throw Exception("'RemoveColumnsWithStops' can only be used on alignment. You may consider using the 'CoerceToAlignment' command."); } if (!codonAlphabet) throw Exception("RemoveColumnsWithStops: requires a codon alphabet."); if (!gCode.get()) { string codeDesc = ApplicationTools::getStringParameter("genetic_code", bppseqman.getParams(), "Standard", "", true, 1); ApplicationTools::displayResult("Genetic Code", codeDesc); gCode.reset(SequenceApplicationTools::getGeneticCode(codonAlphabet->getNucleicAlphabet(), codeDesc)); } for (size_t i = sites->getNumberOfSites(); i > 0; i--) { if (CodonSiteTools::hasStop(sites->getSite(i-1), *gCode)) sites->deleteSite(i - 1); } } // +---------+ // | Get CDS | // +---------+ else if (cmdName == "GetCDS") { if (!codonAlphabet) throw Exception("GetCDS: requires a codon alphabet."); if (!gCode.get()) { string codeDesc = ApplicationTools::getStringParameter("genetic_code", bppseqman.getParams(), "Standard", "", true, 1); ApplicationTools::displayResult("Genetic Code", codeDesc); gCode.reset(SequenceApplicationTools::getGeneticCode(codonAlphabet->getNucleicAlphabet(), codeDesc)); } OrderedSequenceContainer* sc = 0; if (aligned) sc = new VectorSiteContainer(sequences->getAlphabet()); else sc = new VectorSequenceContainer(sequences->getAlphabet()); for (size_t i = 0; i < sequences->getNumberOfSequences(); ++i) { BasicSequence seq = sequences->getSequence(i); size_t len = seq.size(); SequenceTools::getCDS(seq, *gCode, false, true, true, false); if (aligned) { for (size_t c = seq.size(); c < len; ++c) seq.addElement(seq.getAlphabet()->getGapCharacterCode()); } sc->addSequence(seq, false); } delete sequences; sequences = sc; } // +--------------------------+ // | Resolve dotted alignment | // +--------------------------+ else if (actions[a] == "CoerceToAlignment") { SiteContainer* sites = dynamic_cast(sequences); if(! sites) { sites = new VectorSiteContainer(*sequences); delete sequences; sequences = sites; } aligned = true; } else if (actions[a] == "ResolvedDotted") { SiteContainer* sites = dynamic_cast(sequences); if (!sites) { throw Exception("'ResolvedDotted' can only be used on alignment. You may consider using the 'CoerceToAlignment' command."); } const Alphabet* alpha = 0; string alphastr = ApplicationTools::getStringParameter("alphabet", cmdArgs, "DNA", "", false, 1); if (alphastr == "DNA") alpha = &AlphabetTools::DNA_ALPHABET; else if (alphastr == "RNA") alpha = &AlphabetTools::RNA_ALPHABET; else if (alphastr == "Protein") alpha = &AlphabetTools::PROTEIN_ALPHABET; else throw Exception("Resolved alphabet must be one of [DNA|RNA|Protein] for solving dotted alignment."); OrderedSequenceContainer* resolvedCont = SiteContainerTools::resolveDottedAlignment(*sites, alpha); delete sequences; sequences = resolvedCont; } // +---------------------+ // | Keep complete sites | // +---------------------+ else if (cmdName == "KeepComplete") { SiteContainer* sites = dynamic_cast(sequences); if (!sites) { throw Exception("'KeepComplete' can only be used on alignment. You may consider using the 'CoerceToAlignment' command."); } string maxGapOption = ApplicationTools::getStringParameter("maxGapAllowed", cmdArgs, "100%", "", false, 1); if (maxGapOption[maxGapOption.size()-1] == '%') { double gapFreq = TextTools::toDouble(maxGapOption.substr(0, maxGapOption.size()-1)) / 100.; for (size_t i = sites->getNumberOfSites(); i > 0; i--) { map freqs; SiteTools::getFrequencies(sites->getSite(i - 1), freqs); if (freqs[-1] > gapFreq) sites->deleteSite(i - 1); } } else { size_t gapNum = TextTools::to(maxGapOption); for (size_t i = sites->getNumberOfSites(); i > 0; i--) { map counts; SiteTools::getCounts(sites->getSite(i - 1), counts); counts[-1]; //Needed in case this entry does not exist in the map. This will set it to 0. if (counts[-1] > gapNum) sites->deleteSite(i-1); } } } // +-----------------+ // | Invert sequence | // +-----------------+ else if (cmdName == "Invert") { OrderedSequenceContainer* sc = 0; if (aligned) sc = new VectorSiteContainer(sequences->getAlphabet()); else sc = new VectorSequenceContainer(sequences->getAlphabet()); for (size_t i = 0; i < sequences->getNumberOfSequences(); i++) { const Sequence* old = &sequences->getSequence(i); Sequence* seq = SequenceTools::getInvert(*old); sc->addSequence(*seq, false); delete seq; } delete sequences; sequences = sc; } // +------------------+ // | GetCodonPosition | // +------------------+ else if (cmdName == "GetCodonPosition") { unsigned int pos = ApplicationTools::getParameter("position", cmdArgs, 3, "", false, 1); OrderedSequenceContainer* sc = dynamic_cast(SequenceContainerTools::getCodonPosition(*sequences, pos - 1)); delete sequences; if (aligned) { sequences = new VectorSiteContainer(*sc); delete sc; } else { sequences = sc; } } // +-----------------+ // | FilterFromTree | // +-----------------+ else if (cmdName == "FilterFromTree") { unique_ptr tree(PhylogeneticsApplicationTools::getTree(cmdArgs, "")); vector names = tree->getLeavesNames(); OrderedSequenceContainer* reorderedSequences = 0; if (aligned) { reorderedSequences = new VectorSiteContainer(sequences->getAlphabet()); } else { reorderedSequences = new VectorSequenceContainer(sequences->getAlphabet()); } for (size_t i = 0; i < names.size(); ++i) { reorderedSequences->addSequence(sequences->getSequence(names[i]), false); } delete sequences; sequences = reorderedSequences; } // +----------------------+ // | RemoveEmptySequences | // +----------------------+ else if (cmdName == "RemoveEmptySequences") { OrderedSequenceContainer* sc = 0; if (aligned) sc = new VectorSiteContainer(sequences->getAlphabet()); else sc = new VectorSequenceContainer(sequences->getAlphabet()); for (size_t i = 0; i < sequences->getNumberOfSequences(); ++i) { if (SequenceTools::getNumberOfSites(sequences->getSequence(i))!=0) sc->addSequence(sequences->getSequence(i), false); } delete sequences; sequences = sc; } else throw Exception("Unknown action: " + cmdName); } // Write sequences ApplicationTools::displayBooleanResult("Final sequences are aligned", aligned); if (aligned) { SequenceApplicationTools::writeAlignmentFile(*dynamic_cast(sequences), bppseqman.getParams(), "", true, 1); } else { SequenceApplicationTools::writeSequenceFile(*sequences, bppseqman.getParams(), "", true, 1); } delete alphabet; delete sequences; bppseqman.done(); } catch(exception & e) { cout << e.what() << endl; return 1; } return 0; } bppsuite-2.4.1/bppSuite/bppTreeDraw.cpp000066400000000000000000000200271333524216000200670ustar00rootroot00000000000000// // File: bppTreeDraw.cpp // Created by: Julien Dutheil // Created on: Jul Tue 21 13:40 2009 // /* Copyright or © or Copr. Bio++ Development Team This software is a computer program whose purpose is to draw phylogenies. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms. */ // From the STL: #include #include using namespace std; // From bpp-core: #include #include #include #include #include #include #include // From bpp-phyl: #include #include #include #include #include using namespace bpp; /******************************************************************************/ void help() { (*ApplicationTools::message << "__________________________________________________________________________").endLine(); (*ApplicationTools::message << "bpptreedraw parameter1_name=parameter1_value parameter2_name=parameter2_value").endLine(); (*ApplicationTools::message << " ... param=option_file").endLine(); (*ApplicationTools::message).endLine(); (*ApplicationTools::message << " Refer to the Bio++ Program Suite Manual for a list of available options.").endLine(); (*ApplicationTools::message << "__________________________________________________________________________").endLine(); } int main(int args, char ** argv) { cout << "******************************************************************" << endl; cout << "* Bio++ Tree Drawing program, version " << BPP_VERSION << ". *" << endl; cout << "* *" << endl; cout << "* Authors: J. Dutheil Last Modif. " << BPP_REL_DATE << " *" << endl; cout << "******************************************************************" << endl; cout << endl; if (args == 1) { help(); return 0; } try { BppApplication bpptreedraw(args, argv, "BppTreeDraw"); bpptreedraw.startTimer(); // Get the tree to plot: Tree* tree = PhylogeneticsApplicationTools::getTree(bpptreedraw.getParams()); ApplicationTools::displayResult("Number of leaves", TextTools::toString(tree->getNumberOfLeaves())); // Get the graphic device: GraphicDevice* gd = 0; string outputPath = ApplicationTools::getAFilePath("output.drawing.file", bpptreedraw.getParams(), true, false, "", false); ofstream file(outputPath.c_str(), ios::out); string graphicTypeCmd = ApplicationTools::getStringParameter("output.drawing.format", bpptreedraw.getParams(), "Svg"); string graphicType; map graphicTypeArgs; KeyvalTools::parseProcedure(graphicTypeCmd, graphicType, graphicTypeArgs); if (graphicType == "Svg") { gd = new SvgGraphicDevice(file); } else if (graphicType == "Inkscape") { gd = new SvgGraphicDevice(file, true); } else if (graphicType == "Xfig") { gd = new XFigGraphicDevice(file); dynamic_cast(gd)->setFontFlag(XFigGraphicDevice::FONTFLAG_POSTSCRIPT); } else if (graphicType == "Pgf") { gd = new PgfGraphicDevice(file, 0.045); } else throw Exception("Unknown output format: " + graphicType); // Get the tree plotter: TreeDrawing* td = 0; string plotTypeCmd = ApplicationTools::getStringParameter("output.drawing.plot", bpptreedraw.getParams(), "Cladogram"); string plotType; map plotTypeArgs; KeyvalTools::parseProcedure(plotTypeCmd, plotType, plotTypeArgs); if (plotType == "Cladogram") { td = new CladogramPlot(); } else if (plotType == "Phylogram") { td = new PhylogramPlot(); } else throw Exception("Unknown output format: " + plotType); td->setTree(tree); ApplicationTools::displayResult("Plot type", plotType); double xunit = ApplicationTools::getDoubleParameter("xu", plotTypeArgs, 10); double yunit = ApplicationTools::getDoubleParameter("yu", plotTypeArgs, 10); td->setXUnit(xunit); td->setYUnit(yunit); string hOrientation = ApplicationTools::getStringParameter("direction.h", plotTypeArgs, "left2right"); if (hOrientation == "left2right") { dynamic_cast(td)->setHorizontalOrientation(AbstractDendrogramPlot::ORIENTATION_LEFT_TO_RIGHT); } else if (hOrientation == "right2left") { dynamic_cast(td)->setHorizontalOrientation(AbstractDendrogramPlot::ORIENTATION_RIGHT_TO_LEFT); } else throw Exception("Unknown orientation option: " + hOrientation); string vOrientation = ApplicationTools::getStringParameter("direction.v", plotTypeArgs, "top2bottom"); if (vOrientation == "top2bottom") { dynamic_cast(td)->setVerticalOrientation(AbstractDendrogramPlot::ORIENTATION_TOP_TO_BOTTOM); } else if (vOrientation == "bottom2top") { dynamic_cast(td)->setVerticalOrientation(AbstractDendrogramPlot::ORIENTATION_BOTTOM_TO_TOP); } else throw Exception("Unknown orientation option: " + vOrientation); //Plotting option: TreeDrawingSettings tds; BasicTreeDrawingDisplayControler* controler = new BasicTreeDrawingDisplayControler(&tds); controler->registerTreeDrawing(td); bool drawLeafNames = ApplicationTools::getBooleanParameter("draw.leaves", plotTypeArgs, true); bool drawNodesId = ApplicationTools::getBooleanParameter("draw.ids" , plotTypeArgs, false); bool drawBranchLengths = ApplicationTools::getBooleanParameter("draw.brlen" , plotTypeArgs, false); bool drawBootstrapValues = ApplicationTools::getBooleanParameter("draw.bs" , plotTypeArgs, false); controler->enableListener(controler->PROPERTY_LEAF_NAMES, drawLeafNames); controler->enableListener(controler->PROPERTY_NODE_IDS, drawNodesId); controler->enableListener(controler->PROPERTY_BRANCH_LENGTHS, drawBranchLengths); controler->enableListener(controler->PROPERTY_BOOTSTRAP_VALUES, drawBootstrapValues); ApplicationTools::displayBooleanResult("Draw leaf names" , drawLeafNames); ApplicationTools::displayBooleanResult("Draw node ids" , drawNodesId); ApplicationTools::displayBooleanResult("Draw branch lengths" , drawBranchLengths); ApplicationTools::displayBooleanResult("Draw bootstrap values", drawBootstrapValues); //Now draw the tree: gd->begin(); td->plot(*gd); gd->end(); //Finishing things: file.close(); delete controler; delete tree; delete td; delete gd; bpptreedraw.done(); } catch(exception & e) { cout << e.what() << endl; return 1; } return 0; } bppsuite-2.4.1/bppsuite.spec000066400000000000000000000073261333524216000160670ustar00rootroot00000000000000%define _prefix /usr URL: https://github.com/BioPP Name: bppsuite Version: 2.4.1 Release: 1%{?dist} License: CECILL-2.0 Vendor: The Bio++ Project Source: %{name}-%{version}.tar.gz Summary: The Bio++ Program Suite Group: Productivity/Scientific/Other Requires: libbpp-popgen8 = %{version} Requires: libbpp-phyl12 = %{version} Requires: libbpp-seq12 = %{version} Requires: libbpp-core4 = %{version} BuildRoot: %{_builddir}/%{name}-root BuildRequires: cmake >= 2.8.11 BuildRequires: gcc-c++ >= 4.7.0 BuildRequires: groff BuildRequires: texinfo >= 4.0.0 BuildRequires: libbpp-core4 = %{version} BuildRequires: libbpp-core-devel = %{version} BuildRequires: libbpp-seq12 = %{version} BuildRequires: libbpp-seq-devel = %{version} BuildRequires: libbpp-phyl12 = %{version} BuildRequires: libbpp-phyl-devel = %{version} BuildRequires: libbpp-popgen8 = %{version} BuildRequires: libbpp-popgen-devel = %{version} AutoReq: yes AutoProv: yes %if 0%{?mdkversion} %if 0%{?mdkversion} >= 201100 BuildRequires: xz %define compress_program xz %else BuildRequires: lzma %define compress_program lzma %endif %else BuildRequires: gzip %define compress_program gzip %endif %description Bio++ program suite includes programs: - BppML for maximum likelihood analysis, - BppSeqGen for sequences simulation, - BppAncestor for ancestral states reconstruction, - BppDist for distance methods, - BppPars for parsimony analysis, - BppSeqMan for file conversion and sequence manipulation, - BppConsense for building consensus tree and computing bootstrap values, - BppReRoot for tree rerooting. - BppTreeDraw for tree drawing. - BppAlnScore for comparing alignments and computing alignment scores. - BppPopStats for population genetics. - BppMixedLikelioods for computing the site per site likelihoods of submodels from a mixture model. %prep %setup -q %build CFLAGS="$RPM_OPT_FLAGS" CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=%{_prefix} -DCOMPRESS_PROGRAM=%{compress_program}" cmake $CMAKE_FLAGS . make %install make DESTDIR=$RPM_BUILD_ROOT install %clean rm -rf $RPM_BUILD_ROOT %post -p /sbin/ldconfig %postun -p /sbin/ldconfig %files %defattr(-,root,root) %doc AUTHORS.txt COPYING.txt INSTALL.txt ChangeLog %{_prefix}/bin/* %{_prefix}/share/info/*.info* %{_prefix}/share/man/man1/*.1* %changelog * Wed Aug 15 2018 Julien Dutheil 2.4.1-1 * Mon Mar 12 2018 Julien Dutheil 2.4.0-1 * Tue Jun 06 2017 Julien Dutheil 2.3.1-1 * Wed May 10 2017 Julien Dutheil 2.3.0-1 - New BppPopStats program - BppPhySamp is now distributed separately - Several bugs fixed and improvements * Mon Sep 29 2014 Julien Dutheil 2.2.0-1 - Compatibility update. Bio++ Program Suite version number is now indexed on Bio++'s version. - Programs support the --seed argument for setting the random seed. - bppSeqGen suport generic characters as input. - bppPhySamp outputs sampled trees. * Fri Mar 08 2013 Julien Dutheil 0.8.0-1 - New models for proteins (COaLA) - New program bppMixedLikelihoods * Wed Feb 15 2012 Julien Dutheil 0.7.0-1 - More models, sequence formats and bugs fixed. New bppAlnScore program. * Thu Jun 09 2011 Julien Dutheil 0.6.2-1 * Mon Feb 28 2011 Julien Dutheil 0.6.1-1 * Mon Feb 07 2011 Julien Dutheil 0.6.0-1 * Thu Mar 25 2010 Julien Dutheil 0.5.0-1 * Wed Jun 10 2009 Julien Dutheil 0.4.0-1 * Thu Dec 11 2008 Julien Dutheil 0.3.1-1 * Tue Sep 23 2008 Julien Dutheil 0.3.0-1 - Initial spec file. bppsuite-2.4.1/buildBin.sh000077500000000000000000000012721333524216000154410ustar00rootroot00000000000000#! /bin/sh arch=x86_64 #i686 version=2.3.2 strip bppSuite/bppdist strip bppSuite/bpppars strip bppSuite/bppml strip bppSuite/bppseqgen strip bppSuite/bppconsense strip bppSuite/bppseqman strip bppSuite/bppphysamp strip bppSuite/bppreroot strip bppSuite/bppancestor strip bppSuite/bpptreedraw strip bppSuite/bppalnscore strip bppSuite/bppmixedlikelihoods strip bppSuite/bpppopstats tar cvzf bppsuite-${arch}-bin-static-${version}.tar.gz bppSuite/bppdist bppSuite/bpppars bppSuite/bppml bppSuite/bppseqgen bppSuite/bppconsense bppSuite/bppseqman bppSuite/bppphysamp bppSuite/bppreroot bppSuite/bppancestor bppSuite/bpptreedraw bppSuite/bppalnscore bppSuite/bppmixedlikelihoods bppSuite/bpppopstats bppsuite-2.4.1/buildExample.sh000077500000000000000000000001051333524216000163160ustar00rootroot00000000000000#! /bin/sh zip -r bppsuite-examples-0.8.0.zip Examples -x \*.svn\* bppsuite-2.4.1/doc/000077500000000000000000000000001333524216000141155ustar00rootroot00000000000000bppsuite-2.4.1/doc/CMakeLists.txt000066400000000000000000000053011333524216000166540ustar00rootroot00000000000000# CMake script for Bio++ Program Suite # Authors: # Julien Dutheil # Francois Gindraud (2017) # Created: 22/08/2009 # Builds info, html, pdf doc. # Info doc is built and install as part of "all" if makeinfo is found. # Html doc is proposed as a "html" optional target if makeinfo is found. # Pdf doc is proposed as a "pdf" optional target if makeinfo AND texi2dvi are found. find_program (MAKEINFO NAMES makeinfo texi2any DOC "makeinfo doc generator program") if (NOT MAKEINFO) message (STATUS "makeinfo program not found: 'info' and 'html' target disabled (builds info/html doc)") else () message (STATUS "Found ${MAKEINFO}: 'info' and 'html' target enabled (builds info/html doc)") set (input ${CMAKE_CURRENT_SOURCE_DIR}/bppsuite.texi) # Build info page set (output ${CMAKE_CURRENT_BINARY_DIR}/bppsuite.info) add_custom_command ( OUTPUT ${output} COMMAND ${MAKEINFO} --no-split -o ${output} ${input} DEPENDS ${input} COMMENT "Generating info page" VERBATIM ) # Install, and have "info" built with "all" (install needs the file to be built) if (NOT COMPRESS_BIN) # Install uncompressed info page install (FILES ${output} DESTINATION ${CMAKE_INSTALL_INFODIR}) add_custom_target (info ALL DEPENDS ${output}) else () # Compress and install compressed file set (compressed_ouput ${output}.${COMPRESS_EXT}) add_custom_command ( OUTPUT ${compressed_ouput} COMMAND ${COMPRESS_BIN} ${COMPRESS_ARGS} ${output} > ${compressed_ouput} DEPENDS ${output} COMMENT "Compressing info page" VERBATIM ) install (FILES ${compressed_ouput} DESTINATION ${CMAKE_INSTALL_INFODIR}) add_custom_target (info ALL DEPENDS ${compressed_ouput}) endif () # Also provide a "html" target that builds html doc (not installed, and not part of "all"). set (output ${CMAKE_CURRENT_BINARY_DIR}/bppsuite.html) set (makeinfo-css "http://www.w3.org/StyleSheets/Core/Steely") add_custom_command ( OUTPUT ${output} COMMAND ${MAKEINFO} --html --css-ref=${makeinfo-css} --no-split -o ${output} ${input} DEPENDS ${input} COMMENT "Generating html doc" VERBATIM ) add_custom_target (html DEPENDS ${output}) # Provide a "pdf" target that builds pdf doc (not installed, not part of "all"). find_program (TEXIDVI NAMES texi2dvi) if (TEXIDVI) message (STATUS "Found texi2dvi: 'pdf' target enabled (builds pdf doc)") set (output ${CMAKE_CURRENT_BINARY_DIR}/bppsuite.pdf) add_custom_command ( OUTPUT ${output} COMMAND ${MAKEINFO} --pdf --Xopt=--clean -o ${output} ${input} DEPENDS ${input} COMMENT "Generating pdf doc" VERBATIM ) add_custom_target (pdf DEPENDS ${output}) endif () endif () bppsuite-2.4.1/doc/bppsuite.texi000066400000000000000000003454001333524216000166510ustar00rootroot00000000000000\input texinfo @c -*-texinfo-*- @c %**start of header @setfilename bppsuite.info @settitle BppSuite Manual 2.4.0 @documentencoding UTF-8 @afourpaper @dircategory Science Biology Genetics @direntry * bppml: (bppml) Bio++ Maximum Likelihood. * bppseqgen: (bppseqgen) Bio++ Sequence Generator. * bppancestor: (bppancestor) Bio++ Ancestral Sequences and Rates reconstruction. * bppdist: (bppdist) Bio++ Distance Methods. * bpppars: (bpppars) Bio++ Maximum Parsimony. * bppconsense: (bppconsense) Bio++ Consensus Trees. * bppreroot: (bppreroot) Bio++ Serial Tree Re-rooting. * bppseqman: (bppseqman) Bio++ Sequences Manipulation. * bppalnscore: (bppalnscore) Bio++ Alignment Scoring. * bpppopstats: (bpppopstats) Bio++ Population Genetics. * bpptreedraw: (bpptreedraw) Bio++ Tree Drawing. @end direntry @c %**end of header @copying This is the manual of the Bio++ Program Suite, version 2.4.0. Copyright @copyright{} 2007-2018 Bio++ development team @end copying @titlepage @title BppSuite Manual @author Julien Dutheil, Laurent Guéguen @author @email{dutheil@@evolbio.mpg.de} @c The following two commands start the copyright page. @page @vskip 0pt plus 1fill1 @insertcopying @end titlepage @c Output the table of contents at the beginning. @contents @ifnottex @node Top, Introduction, (dir), (dir) @top The Bio++ Program Suite Manual @insertcopying @menu * Introduction:: Introducing the Bio++ Program Suite and this manual. * Syntax:: A general description of the syntax used to communicate with the programs. * Common:: Common options shared by several programs. * Reference:: The exhaustive list of options available for all programs in the Bio++ Program Suite. @detailmenu --- The Detailed Node Listing --- Common options encountered in several programs. * Alphabet:: Alphabets and genetic codes. * Sequences:: Loading sequences/alignments. * Tree:: Loading trees. * AlphabetIndex:: Setting biochemical properties and distances. * Process:: * Distribution:: Setting of the discrete distributions. * Estimation:: Estimating parameters by maximizing a likelihood function. * WritingSequences:: Writing sequences/alignments to files. * WritingTrees:: Writing trees to files. Process specification * Model:: * Non-homogeneity:: Specific declaration of non-homogeneous modelling. * FrequenciesSet:: Frequencies * Rates:: Rates across sites * Linking:: Setting up the substitution model * Nucleotide:: Nucleotide models * Protein:: Protein models * Miscellaneous:: Miscellaneous models * Codon:: Codon models * Multiple:: General multiple site models * Meta:: Meta models * Mixture:: Mixture of models * Conditioned:: Models conditioned by events Bio++ Program Suite Reference * bppml:: Bio++ Maximum Likelihood. * bppseqgen:: Bio++ Sequence Generator. * bppancestor:: Bio++ Ancestral Sequences and Rates reconstruction. * bppmixedlikelihoods:: Bio++ Site-Likelihoods Inside Mixed Models. * bppdist:: Bio++ Distance Methods. * bpppars:: Bio++ Maximum Parsimony. * bppconsense:: Bio++ Consensus Trees. * bppreroot:: Bio++ Serial Tree Re-rooting. * bppseqman:: Bio++ Sequences Manipulation. * bppalnscore:: Bio++ Alignment Scoring. * bpppopstats:: Bio++ Population Genetics Statistics. * bpptreedraw:: Bio++ Tree Drawing. @end detailmenu @end menu @end ifnottex @c ------------------------------------------------------------------------------------------------------------------ @node Introduction, Syntax, Top, Top @chapter Introduction The Bio++ Program Suite is a package of programs using the Bio++ libraries and dedicated to Phylogenetics and Molecular Evolution. All programs are independent, but can be combined to perform rather complex analyses. These programs use the interface helper tools of the libraries, and hence share the same syntax. They also have several options in common, which may also be shared by third-party software. This manual was hence split into three parts: @table @emph @item Bio++ option file syntax A general description of the language used to interact with the programs. @item Shared options A more detailed description about several options that are encountered in several programs. This includes input/output of data and model specifications. @item The Bio++ Program Suite reference Include a reference of all available options for each program in the package. @end table @c ------------------------------------------------------------------------------------------------------------------ @node Syntax, Common, Introduction, Top @chapter Syntax description @section Calling the programs and writing the option files. The programs in the Bio++ Program Suite are command line-driven. Arguments may be passed as @command{parameter=value} options, either directly to the command line or using an option file: @cartouche @example @{program@} parameter1=value1 parameter2=value2 ... parameterN=valueN @end example @end cartouche or @cartouche @example @{program@} param=option_file @end example @end cartouche where @{program@} is the name of the program to use (bppml, bppseqgen, etc.). Option files contain @command{parameter=value} lines, with only one parameter per line. They can be written from scratch using a regular text editor, but since these files can potentially turn to be quite complex, it is probably wiser to start with a sample provided along with the program (if any!). Extra-space may be included between parameter names, equal sign and value: @cartouche @example first_parameter = value1 second_parameter = value2 @end example @end cartouche and lines can be broken using the backslash character: @cartouche @example parameter = value1,\ value2,\ value3 @end example @end cartouche Comment may be included, in either scripting format: @cartouche @example # This is a comment @end example @end cartouche C format: @cartouche @example /* This is a comment */ @end example @end cartouche or C++ format: @cartouche @example // This is a comment @end example @end cartouche Command line and file options may be combined: @cartouche @example @{program@} param=option_file parameterX=valueX @end example @end cartouche In case @command{parameterX} is specified in both option file and command line, the command line value will be used. This allows to run the programs several times by changing a single option, like the name of the data set for instance. Option files can be nested, by using @command{param=nestedoptionfile} within an option file, as with the command line. It is possible to use this option as often as needed, this will load all the required option files. @section Different types of options The next chapters describe the whole set of options available in BppSuite. For each parameter, the type of parameter value expected is defined as: @table @command @item @{chars@} A character chain @item @{path@} A file path, which may be absolute or related to the current directory @item @{int@} An integer @item @{int@}, @{int>0@}, @{int>=0@}, @{int[2,10]@} An integer, a positive integer, a positive non-null integer, an integer falling between 2 and 10 @item @{real@}, @{real>0@}, etc A real number, a positive real number, etc. @item @{boolean@} A Boolean value, which may be one of 'yes', 'no', 'true' or 'false' @item @{xxx|yyy|zzz@} A set of allowed values @item @{list@} A list of values of specified type, separated by comas. @end table If an option availability or choice depends on another parameters, it will be noted as @example parameter1=@{xxx|yyy|zzz@} parameter2=@{chars@} [[parameter1=zzz]] @end example meaning that parameter2 is available only if parameter1 is set to 'zzz'. Any optional argument will be noted within hooks []. In some cases, the argument value is more complexe and follows the 'keyval' syntax. This syntax will be quite familiar for users using languages like R, Python, or certain LaTeX packages. A keyval procedure is a name that does no contain any space, together with some arguments within parentheses. The arguments take the form @command{key=value}, separated by comas: @cartouche @example parameter=Function(name1=value1, name2=value2) @end example @end cartouche Space characters are allowed around the '=' and ',' ponctuations. @section Variables It is possible to recall anywhere the value of an option by using $(parameter). @cartouche @example topo.algo = NNI topo.algo_nni.method = phyml output.tree.file = MyData_$(topo.algo)_$(topo.algo_nni.method).dnd @end example @end cartouche You can use this syntax to define global variables: @cartouche @example data=MyData input.sequence.file=$(data).fasta input.tree.file=$(data).dnd output.infos=$(data).infos @end example @end cartouche Important note: it is not possible to use a macro with the 'param' option. This is because all nested option files are parsed before the variable resolution. Writing @command{param=$(model1).bpp} will not work, but this allows the user to override variables in nested files, as with the command line. For instance: @cartouche @example #Option file 1: param=options2.bpp input.sequence.file=$(data).fasta input.sequence.format=Fasta @end example @end cartouche @cartouche @example #Option file 2: data=LSU #etc @end example @end cartouche @c ------------------------------------------------------------------------------------------------------------------ @node Common, Reference, Syntax, Top @chapter Common options encountered in several programs. @c ------------------------------------------------------------------------------------------------------------------ @menu * Alphabet:: Alphabets and genetic codes. * Sequences:: Loading sequences/alignments. * Tree:: Loading trees. * AlphabetIndex:: Setting biochemical properties and distances. * Process:: * Distribution:: Setting of the discrete distributions. * Estimation:: Estimating parameters by maximizing a likelihood function. * WritingSequences:: Writing sequences/alignments to files. * WritingTrees:: Writing trees to files. @end menu @node Alphabet, Sequences, Common, Common @section Setting alphabet and genetic code @table @command @item alphabet = @{DNA|RNA|Protein|Binary|Word(letter=@{DNA|RNA|Protein@},length=@{int@})| Codon(letter=@{DNA|RNA@})@} The alphabet to use when reading sequences. DNA and RNA alphabet can in addition take an argument: @table @command @item bangAsgap=@{bool@} Tell is exclamation mark should be considered as a gap character. The default is to consider it as an unknown character such as 'N' or '?'. @end table @item genetic_code = @{translation table@} The genetic code used for codon alphabet, where 'translation table' specifies the code to use, either as a text description, or as the NCBI number. The following table give the currently implemented codes with their corresponding names: @multitable @columnfractions 0.5 0.5 @item Standard @tab 1 @item VertebrateMitochondrial @tab 2 @item YeastMitochondrial @tab 3 @item MoldMitochondrial @tab 4 @item InvertebrateMitochondrial @tab 5 @item EchinodermMitochondrial @tab 9 @item AscidianMitochondrial @tab 13 @end multitable @end table The states of the alphabets are in alphabetical order. For the proteic alphabet, the amino-acid are in the order of their 3-letters code (ALA, ARG, ASN, ...). @c ------------------------------------------------------------------------------------------------------------------ @node Sequences, Tree, Alphabet, Common @section Reading sequences @table @command @item input.sequence.file=@{path@} The sequence file to use. Depending on the program, these sequences have or do not have to be aligned. @item input.sequence.format = @{sequence format description@} The sequence file format. @item input.site.selection = @{list of integers@} Will only consider sites in the given list of positions, in extended format : positions separated with ",", and "i-j" for all positions between i and j, included. @item input.site.selection = @{Sample(n=@{integer@} [, replace=@{true@}])@} Will consider @{n@} random sites, with optional replacement. @end table Since Bio++ Program Suite version 0.4.0, the format description uses the keyval syntax. The format is a function, with optional parameters: @table @command @item Fasta(extended=@{bool@}, strictNames=@{bool@}) The fasta format. The argument @command{extended}, default to 'no', allows to enable the HUPO-PSI extension of the format. The argument @command{strict_names}, default to 'no', specifies that only the first word in the fasta header is used as a sequence names, the rest of the header being considered as comments. @item Mase(siteSelection=@{chars@}) The Mase format (as read by Seaview and Phylo_win for instance), with an optional site selection name. @item Phylip(order=@{interleaved|sequential@}, type=@{classic|extended@}, split=@{spaces|tab@}) The Phylip format, with several variations. The argument @command{order} distinguishes between sequential and interleaved format, while the option @command{type} distinguished between the plain old Phylip format and the more recent extension allowing for sequence names longer than 10 characters, as understood by PAML and PhyML. Finally, the @command{split} argument specifies the type of character that separates the sequence name from the sequence content. The conventional option is to use one (classic) or more (extended) spaces, but tabs can also be used instead. @item Clustal(extraSpaces=@{int@}) The Clustal format. In its basic set up, sequence names do not have space characters, and one space splits the sequence content from its name. The parser can however be configured to allow for spaces in the sequence names, providing a minimum number of space characters is used to split the content from the name. Setting @command{extraSpaces} to 5 for instance, the sequences are expected to be at least 6 spaces away for their names. @item Dcse() The DCSE alignment format. The secondary structure annotation will be ignored. @item Nexus() The Nexus alignment format. Only very basic support is provided. @end table For programs that do not require the sequences to be aligned, the following formats are also available: @table @command @item GenBank() Very basic support: only retrieves the sequence content for now, all features are ignored. @end table Basic operations can be performed on the sequences: @table @command @item input.sequence.sites_to_use = @{all|nogap|complete@} This option only works if the program requires an alignment. Tells which sites to use. The @option{nogap} option removes all sites containing at least one gap, and the @option{complete} option removes all sites containing at least one gap or one generic character, as 'X' for instance. @item input.sequence.remove_stop_codons = @{boolean@} This option only works if the alphabet is a codon alphabet. Removes the sites where there is a stop codon (default: 'yes'). @item input.sequence.max_gap_allowed=100% This option only works if the program requires an alignment. Only works when the @option{all} option is selected. It specifies the maximum amount of gap allowed per site, as a number of sequence or a percentage. Sites not matching the criterion will not be included in the analysis, but the original site numbering will be used in the output files (if relevant). @item input.sequence.max_unresolved_allowed=100% This option only works if the program requires an alignment. Only works when the @option{all} option is selected. It specifies the maximum amount of unresolved states per site, as a number of sequence or a percentage. Sites not matching the criterion will not be included in the analysis, but the original site numbering will be used in the output files (if relevant). @end table @c ------------------------------------------------------------------------------------------------------------------ @node Tree, AlphabetIndex, Sequences, Common @section Reading trees @table @command @item input.tree.file = @{path@} The phylogenetic tree file to use. @item input.tree.format = @{Newick|Nexus|NHX@} The format of the input tree file. @end table In case the input tree does not specify node identifiers, some will be generated automatically. Nodes identifiers can be outputed using the following option: @table @command @item output.tree_ids.file = @{@{path@}|none@} A tree file in newick format, with node ids instead of bootstrap values, and leaf names with their id as suffix. @end table In case it is supported by the program, the use of that option will cause the program to exit just after producing the tagged tree. Some programs may require that your file contains several trees. The corresponding options are then: @table @command @item input.trees.file = @{path@} The file containing multiple trees. @item input.trees.format = @{Newick|Nexus|NHX@} The format of the input tree file. @end table @c ------------------------------------------------------------------------------------------------------------------ @node AlphabetIndex, Process, Tree, Common @section Specifying biochemical properties and distances Some methods require an "alphabet index" to be specified. Alphabet indexes associate a value with each alphabet state (Index1, e.g. a biochemical property) or for a pair of states (Index2, e.g. a biochemical distance). This section describes the supported indexes: @subsection Index1 @table @command @item None If no index should be used. @item Surface, Mass, Volume, Charge @{AA@} Basic amino acids properties. @item GranthamPolarity, GranthamVolume @{AA@} Grantham's polarity and volume index. @item KleinCharge @{AA@} Klein's charge. @item ChouFasmanAHelix, ChouFasmanBSheet, ChouFasmanTurn @{AA@} Chou and Fasmani score for secondary structure prediction. @item ChenGuHuangHydrophobicity @{AA@} Hydrophobicity according to Chen, Gu and Huang. @item SEALow, SEAMedium, SEAHigh @{AA@} Solvent Exposed Area, percent of amino acids having a SEA below 10, between 10 and 30, or higher than 30, respectively. @item User A user defined Index1, from a file in the AAIndex1 syntax. The input file is specified using the @command{file=@{path@}} argument. @command{file} @end table @subsection Index2 @table @command @item None If no index should be used. @item Blosum50 @{AA@} The BLOSUM 50 amino acid distance matrix. @item Grantham, Miyata @{AA@} Two biochemical distance matrices. Both accept an optional argument @command{symmetrical=@{boolean@}} allowing to specify if the matrix should be symmetric or not. If not, the distance measure will be signed. @item Diff Allow to compute a distance matrix by taking the difference for, each pair of state, of an Index1 value. The Index1 to use is specified using the @command{index1=@{Index1 description@}} argument. An additional argument allow to specify whether the resulting matrix should be symetric (@command{symmetrical=@{boolean@}}): if so, the absolute difference will be used. Alternatively, the distance will be signed and d[i,j] = - d[j,i]. @item User A user defined Index2, from a file in the AAIndex2 syntax. The input file is specified using the @command{file=@{path@}} argument. The @command{symmetrical=@{boolean@}} argument can be used to specify whether distances should be signed or not. @end table @c ------------------------------------------------------------------------------------------------------------------ @node Process, Distribution, AlphabetIndex, Common @section Process specification @menu * Model:: * Non-homogeneity:: Specific declaration of non-homogeneous modelling. * FrequenciesSet:: Frequencies * Rates:: Rates across sites * Linking:: @end menu The substitution model specification over the tree is set up in different parts. @table @command @item nonhomogeneous = @{no|one_per_branch|general@} Set the type of model. The @option{no} option is used for homogeneous models. The @option{one_per_branch} option is used as a short cut for setting branch models (for instance Galtier and Gouy 97 for branch GC content, or PAML branch model), and the @option{general} option for the more general case, including PAML clade models. In either of the last two cases, the model is potentially non-stationary, that is, possibly not at the equilibrium and hence includes the root frequencies as additional parameters. If the substitution model is not the same across the tree, then the model is also non-homogeneous. @end table In combination with those models, one can also specify a distribution of site-specific rate. @node Model, Non-homogeneity, Process, Process @subsection Setting up the substitution model @menu * Nucleotide:: Nucleotide models * Protein:: Protein models * Miscellaneous:: Miscellaneous models * Codon:: Codon models * Multiple:: General multiple site models * Meta:: Meta models * Mixture:: Mixture of models * Conditioned:: Models conditioned by events @end menu @table @command @item model = @{model description@} A description of the substitution model to use, using the keyval syntax. @end table From version 0.4.0 of BppSuite, the model specification uses a completely new syntax, based on the keyval (key = value) scheme. The old option files will hence not be compatible with new version of the software. The new syntax however is hopefully more intuitive, and more generalizable, so that few changes are expected when new models will be built. The substitution model is a function, potentially including parameters. The following table lists the set of usable functions, and their parameters. Many models have a set of optional parameters denoted here as "equilibrium frequencies" that are used to initialize the parameters of the model related with the equilibrium frequencies. These options are: @table @command @item initFreqs=values(@{real]0,1[@},...,@{real]0,1[@}) The equilibrium frequency is set equal (as much as possible) to the given frequencies. Those frequencies are given in the same order as the alphabet, and they must sum 1. @item initFreqs=observed The equilibrium frequency is set equal (as much as possible) to the observed frequencies. @item initFreqs.observedPseudoCount=@{integer@} a peusocount integer added to all counts of letters (or words), when the frequencies are computed from observed data. @end table @node Nucleotide, Protein, Model, Model @subsubsection Nucleotide models @table @command @item JC69 The Jukes and Cantor model. This model has no additional parameter. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1JCnuc.html#details, Bio++ description, Bio++ description}. @item K80([kappa=@{real>0@}]) The Kimura 2 parameters model. @var{kappa} is the transition over transversion ratio. Default: @var{kappa}=1. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1K80.html#details, Bio++ description, Bio++ description}. @item F84([kappa=@{real>0@}, theta=@{real]0,1[@}, theta1=@{real]0,1[@},theta2=@{real]0,1[@}, "equilibrium frequencies"] ) Felsenstein's 1984 substitution model, with transition/transversion ratio and 4 distinct equilibrium frequencies, set using three independent parameters: @var{theta} is the GC content, @var{theta1} is the proportion of G / (G + C) and @var{theta2} is the proportion of A / (A + T or U). See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1F84.html#details, Bio++ description, Bio++ description}. @item HKY85([kappa=@{real>0@}, theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@}, "equilibrium frequencies"]) Hasegawa, Kishino and Yano 1985's substitution model. The model is similar to @command{F84}, but with a different implementation. The @var{kappa} parameter used here is comparable to the one in @command{K80}. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1HKY85.html#details, Bio++ description, Bio++ description}. @item T92([kappa=@{real>0@}, theta=@{real]0,1[@} ,"equilibrium frequencies"]) Tamura 1992's model for nucleotides, similar to @command{HKY85}, yet assuming that the frequencies of A = T/U and G = C. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1T92.html#details, Bio++ description, Bio++ description}. @item TN93([kappa1=@{real>0@}, kappa2=@{real>0@}, theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@}, "equilibrium frequencies"]) Tamura and Nei 1993's model, similar to @command{HKY85}, but allowing for two distinct transition/transversion ratios. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1TN93.html#details, Bio++ description, Bio++ description}. @item GTR([a=@{real>0@}, b=@{real>0@}, c=@{real>0@}, d=@{real>0@}, e=@{real>0@}, theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@} ,"equilibrium frequencies"]) The General Time-Reversible substitution model. Parameters @var{a}, @var{b}, @var{c}, @var{d}, @var{e} are the entries of the exchangeability matrix. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1GTR.html#details, Bio++ description, Bio++ description}. @item L95([beta=@{real>0@}, gamma=@{real>0@}, delta=@{real>0@}, theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@} ,"equilibrium frequencies"]) The strand-symmetric model of Lobry 1995, for nucleotides. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1L95.html#details, Bio++ description, Bio++ description}. @item SSR([beta=@{real>0@}, gamma=@{real>0@}, delta=@{real>0@}, theta=@{real]0,1[@}]) The strand-symmetric reversible model, for nucleotides. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1SSR.html#details, Bio++ description, Bio++ description}. @item RN95([thetaR=@{real]0,1[@}, thetaC=@{real]0,1[@}, thetaG=@{real]0,1[@}, kappaP=@{real[0,1[@}, gammaP=@{real[0,1[@}, sigmaP=@{real>1@}, alphaP=@{real>1@}]) The model described by Rhetsky and Nei, where the only hypothesis is that the transversion rates are only dependent of the target nucleotide. This model is not reversible. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1RN95.html#details,Bio++ description, Bio++ description}. @item RN95s([thetaA=@{real]0,0.5[@}, gamma=@{real]0,0.5[@}, alphaP=@{real>1@}]) The instersection of models RN95 and L95. The two hypotheses are that the transversion rates are only dependent of the target nucleotide, and strand symmetry. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1RN95s.html#details,Bio++ description, Bio++ description}. @end table @node Protein, Miscellaneous, Nucleotide, Model @subsubsection Protein models @table @command @item JC69 The Jukes and Cantor model. This model has no additional parameter. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1JCprot.html#details, Bio++ description, Bio++ description}. @item DSO78 Protein substitution model, using the dcmutt implementation of Kosiol and Goldman 2005. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1DSO78.html#details, Bio++ description, Bio++ description}. @item JTT92 Protein substitution model, using the dcmutt implementation of Kosiol and Goldman 2005. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1JTT92.html#details, Bio++ description, Bio++ description}. @item WAG01 Protein substitution model, from Whelan & Goldman 2001. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1WAG01.html#details, Bio++ description, Bio++ description}. @item LG08 Protein substitution model, from Le & Gascuel 2008. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1LG08.html#details, Bio++ description, Bio++ description}. @item LLG08_EX2([relrate1=@{real]0,1[@}, relproba1=@{real]0,1[@}]) Protein substitution model, from Le, Lartillot & Gascuel 2008. @xref{Mixture}, for the meaning of the variables. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1LLG08__EX2.html#details, Bio++ description, Bio++ description}. @item LLG08_EX3([relrate1=@{real]0,1[@}, relrate2=@{real]0,1[@}, relproba1=@{real]0,1[@}, relproba2=@{real]0,1[@}]) Protein substitution model, from Le, Lartillot & Gascuel 2008. @xref{Mixture}, for the meaning of the variables. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1LLG08__EX3.html#details, Bio++ description, Bio++ description}. @item LLG08_EHO([relrate1=@{real]0,1[@}, relrate2=@{real]0,1[@}, relproba1=@{real]0,1[@}, relproba2=@{real]0,1[@}]) Protein substitution model, from Le, Lartillot & Gascuel 2008. @xref{Mixture}, for the meaning of the variables. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1LLG08__EHO.html#details, Bio++ description, Bio++ description}. @item LLG08_UL2([relrate1=@{real]0,1[@}, relproba1=@{real]0,1[@}]) Protein substitution model, from Le, Lartillot & Gascuel 2008. @xref{Mixture}, for the meaning of the variables. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1LLG08__UL2.html#details, Bio++ description, Bio++ description}. @item LLG08_UL3([relrate1=@{real]0,1[@}, relrate2=@{real]0,1[@}, relproba1=@{real]0,1[@}, relproba2=@{real]0,1[@}]) Protein substitution model, from Le, Lartillot & Gascuel 2008. @xref{Mixture}, for the meaning of the variables. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1LLG08__UL3.html#details, Bio++ description, Bio++ description}. @item LGL08_CAT(nbCat=@{[10,20,30,40,50,60]@}, [relrate1=@{real]0,1[@}, relrate2=@{real]0,1[@}, ..., relproba1=@{real]0,1[@}, relproba2=@{real]0,1[@}, ...] )) CAT protein substitution model, from Le, Gascuel & Lartillot 2008, with a given number (@var{nbCat}) of profiles. @xref{Mixture}, for the meaning of the variables. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1LGL08__CAT.html#details, Bio++ description, Bio++ description}. @item LGL08_CAT_C@{[1,...,nbCat]@}(nbCat=@{[10,20,30,40,50,60]@}) Submodel of a given CAT Protein substitution model, from Le, Gascuel & Lartillot 2008, with a given number (@var{nbCat}) of profiles. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1LGL08__CAT.html#details, Bio++ description, Bio++ description}. @item DSO78+F([theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@}, ... ,"equilibrium frequencies"]) Protein substitution model, using the dcmutt implementation of Kosiol and Goldman 2005 and free equilibrium frequencies. The @var{thetaX} are frequencies parameters, where X is 1 to 19. Parameter @var{theta1} is the proportion of A, @var{theta2} is the proportion of R over (1-A), @var{theta3} the proportion of N over (1-A-R), etc. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1DSO78.html#details, Bio++ description, Bio++ description}. @item JTT92+F([theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@}, ..., "equilibrium frequencies"]) Protein substitution model, using the dcmutt implementation of Kosiol and Goldman 2005 and free equilibrium frequencies. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1JTT92.html#details, Bio++ description, Bio++ description}. @item WAG01+F([theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@}, ..., "equilibrium frequencies"]) Protein substitution model, from Whelan & Goldman 2001, and free equilibrium frequencies. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1WAG01.html#details, Bio++ description, Bio++ description}. @item LG08+F([theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@}, ..., "equilibrium frequencies"]) Protein substitution model, from Le & Gascuel 2008, and free equilibrium frequencies. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1LG08.html#details, Bio++ description, Bio++ description}. @item Empirical(name=@{chars@}, file=@{path@}) Build a protein substitution model from a file in PAML format, and use 'name' as a namespace for parameters. @item Empirical+F(name=@{chars@}, file=@{path@}, [theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@}, ..., "equilibrium frequencies"]) Build a protein substitution model from a file in PAML format, and use free equilibrium frequencies. 'name' will be used as a parameter namespace, including for frequencies. @end table @node Miscellaneous, Codon, Protein, Model @subsubsection Miscellaneous models @table @command @item Binary([kappa=@{real>0@} ,"equilibrium frequencies"]) Build the model on binary alphabet, where @var{kappa} is the relative proportion of 1 over 0 in the equilibrium distribution. Default: @var{kappa}=1. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1BinarySubstitutionModel.html#details, Bio++ description, Bio++ description}. @end table @node Codon, Multiple, Miscellaneous, Model @subsubsection Codon models Some codon models also take as argument a @var{frequencies} option specifying the equilibrium frequencies of the model. Any frequencies description can be used here, but the syntax also supports options similar to the ones used in the PAML software: @itemize @item F0: all frequencies are assumed to be fixed and equal to 1/61, 0 for stop codons. @item F1X4: 4 distinct frequencies are used, with parameters theta, theta1, theta2 (@xref{Frequencies sets}, ``Full'' method). @item F3X4: 4 distinct frequencies are used for each position, resulting in 9 parameters in total (3 independent ``Full'' frequencies set). @item F61: free equilibrium frequencies, stop codons set to 0. @end itemize An optional option @var{mgmtStopCodon} can be set to define how the frequencies computed to stop codons in the case of F1X4 et F3X4 are distributed to other codons. @itemize @item uniform : each stop frequency is distributed evenly @item linear : each stop frequency is distributed to the neighbour codons (ie 1 substitution away), in proportion to each target codon frequency. @item quadratic (default): each stop frequency is distributed to the neighbour codons (ie 1 substitution away), in proportion to the square of each target codon frequency. @end itemize The same words can be used to specify root frequencies for codon models, in the case of non stationarity. @table @command @item GY94([kappa=@{real>0@}, V=@{real>0@}, "equilibrium frequencies"]) Goldman and Yang (1994) substitution model for codons (default values: @var{kappa}=1 and @var{V}=10000). See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1GY94.html#details, Bio++ description, Bio++ description}. @item MG94([rho=@{real>0@}, "equilibrium frequencies"]) Muse and Gaut (1994) substitution model for codons (default values: @var{rho}=1). See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1MG94.html#details, Bio++ description, Bio++ description}. @item YN98([kappa=@{real>0@}, omega=@{real>0@}, "equilibrium frequencies"]) Yang and Nielsen (1998) substitution model for codons (default values: @var{kappa}=1 and @var{omega}=1). See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1YN98.html#details, Bio++ description, Bio++ description}. @item YNGP_M0([kappa=@{real>0@}, omega=@{real>0@}, "equilibrium frequencies"]) The M0 model of PAML, ie the same as YN98. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1YN98.html#details, Bio++ description, Bio++ description}. @item YNGP_M1([kappa=@{real>0@}, omega=@{real>0@}, p0=@{real>0 and <1 @}, "equilibrium frequencies"]) The M1a model of PAML, see Yang, Z., R. Nielsen, N. Goldman, and A.-M. K. Pedersen (2000) (default values: @var{kappa}=1, @var{p0}=0.5, @var{omega}=0.5). See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1YNGP__M1.html#details, Bio++ description, Bio++ description}. @item YNGP_M2([kappa=@{real>0@}, omega0=@{real>0 and <1@}, theta1=@{real>0 and <1 @}], omega1=@{real>1@}, theta2=@{real>0 and <1 @}, "equilibrium frequencies"]) The M2a model of PAML, see Yang, Z., R. Nielsen, N. Goldman, and A.-M. K. Pedersen (2000), with p0=theta1 and p1=(1-theta1)*theta2 (default values: @var{kappa}=1, @var{theta1}=0.33333, @var{theta2}=0.5, @var{omega0}=0.5, @var{omega2}=0.5). See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1YNGP__M2.html#details, Bio++ description, Bio++ description}. @item YNGP_M3([n=@{integer>0@}, kappa=@{real>0@}, omega0=@{real>0 and <1@}, delta1=@{real>0@}, ..., delta@var{n-1}=@{real>0@}, theta1=@{real>0 and <1 @}, ..., theta@var{n-1}1=@{real>0 and <1 @}, "equilibrium frequencies"]) The M3 model of PAML, see Yang, Z., R. Nielsen, N. Goldman, and A.-M. K. Pedersen (2000), with @var{n} discrete values, with p0=theta1 and pk=(1-theta1)*...*(1-thetak)*theta(k+1), and omegak=omega0+delta1+....+deltak (default values: @var{n}=3, @var{kappa}=1, @var{thetak}=1/(n-k+1), @var{omega0}=0.5, @var{deltak}=0.5). See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1YNGP__M3.html#details, Bio++ description, Bio++ description}. @item YNGP_M7(n=@{integer>0@}, kappa=@{real>0@}, p=@{real>1@}, q=@{real>1 @}, "equilibrium frequencies"]) The M7 model of PAML, see Yang, Z., R. Nielsen, N. Goldman, and A.-M. K. Pedersen (2000), with the Beta distribution discretized in @var{n} classes (default values: @var{kappa}=1, @var{p}=2, @var{q}=2). See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1YNGP__M7.html#details, Bio++ description, Bio++ description}. @item YNGP_M8(n=@{integer>0@}, [kappa=@{real>0@}, omegas=@{real>1@}, p0=@{real>0@},p=@{real>1@}, q=@{real>1 @}, "equilibrium frequencies"]) The M8 model of PAML, see Yang, Z., R. Nielsen, N. Goldman, and A.-M. K. Pedersen (2000), with the Beta distribution discretized in @var{n} classes (default values: @var{kappa}=1, @var{p}=2, @var{q}=2, @var{p0}=0.5, @var{omegas}=2). See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1YNGP__M8.html#details, Bio++ description, Bio++ description}. @end table It is also possible to setup more specific models, by specifying a nucleotide model for each position. Model parameters names then take the form of ._.. In the following models, the arguments @var{model} and @var{model@{i@}} are for descriptions of models on bases. @itemize @item If the argument is @var{model}, the @emph{same} single site model is used on all positions (ie the parameters are shared between all positions). @item If the arguments are @var{model1}, @var{model2}, @var{model3}, each single site model stands for a single-site substitution model. In that case, all single site models parameters are position dependent. @end itemize Each single site model is normalized and the substitution rates between codons that differ on more than one letter are null. The generator is first computed with these models and parameters on the whole triplet alphabet, and then the substitution rates to and from stop codons are set to zero and the generator is normalized with this modification. The model names est defined through several words that can be mixed together to build models at hand. Some words are exclusive. The model description must begin with @var{Codon}. @var{Rate} and @var{Prot} and @var{Dist} words define how the models are mixed, either with specific rates, or using proteic models, or with non-synonymous vs synonymous substitution rates. They are exclusive, and one of the three must be used. The default model is @var{Rate}. @table @command @item Rate(model... [, relrate1=@{real>0@}, relrate2=@{real>0@}]) Substitution model on codons with position specific evolution rates. Arguments @var{relrate@{i@}} stands for the relative substitution rates of the sites. Default: @var{relrate@{i@}=1/@{4-i@}}, such that the rate of each site is 1/3. @cartouche @example alphabet=Codon(letter=DNA) genetic_code=Standard model=CodonRate(model=T92) @end example @end cartouche builds a model on codons, such all sites follow the same T92 model. The parameters names are @var{CodonRate.123_T92.kappa}, @var{CodonRate.relrate1}, @var{CodonRate.relrate2}. @cartouche @example alphabet=Codon(letter=DNA) genetic_code=Standard model=CodonRate(model1=T92, model2=T92, model3=JC69) @end example @end cartouche builds a model on codons, such that first and second sites follow independent T92 models, and third site follows a JC69 model. Then the parameters names are @var{CodonRate.1_T92.kappa}, @var{CodonRate.2_T92.kappa}, @var{CodonRate.relrate1}, @var{CodonRate.relrate2}, and can be initialized as is: @cartouche @example model=CodonRate(model1=T92(theta=0.5, kappa=2), \ model2=T92(theta=0.4, kappa=2), model3=JC69) @end example @end cartouche See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1CodonRateSubstitutionModel.html#details, Bio++ description, Bio++ description}. @item Dist(model...[, beta=@{real>0@}]) Substitution model on codons that takes into account the difference between synonymous and non-synonymous substitutions. Optional argument @var{beta} is the ratio between non-synonymous substitution rate and synonymous substitution rate. Default value: 1. @cartouche @example alphabet=Codon(letter=DNA) model=CodonDist(model=T92) @end example @end cartouche builds a model on codons, such all sites follow the same T92 model. The parameters names are @var{CodonDist.123_T92.kappa} and @var{CodonDist.beta}. @cartouche @example alphabet=Codon(letter=DNA, type=Standard) model=CodonDist(model1=T92, model2=T92, model3=JC69) @end example @end cartouche builds a model on codons, such that first and second sites follow independent T92 models, and third site follows a JC69 model. Then the parameters names are @var{CodonDist.1_T92.kappa}, @var{CodonDist.2_T92.kappa}, @var{CodonDist.beta}. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1CodonDistanceSubstitutionModel.html#details, Bio++ description, Bio++ description}. @item Prot(model..., protmodel=@{proteic model name@}[, beta=@{real>0@}]) Substitution model on codons that takes into account the substitution rates in a protein model. Those rates are multiplied by a non-synonymous susbtitution factor, aka @var{beta}. @var{Prot} and @var{Dist} words are exclusive. Optional argument @var{beta} is the ratio between average substitution rate between amino-acids and synonymous substitution rate. Default value: 1. @cartouche @example alphabet=Codon(letter=DNA) genetic_code=Standard model=CodonProt(model=T92, protmodel=LG08) @end example @end cartouche builds a model on codons, such all sites follow the same T92 model, and amino-acid rates are proportional to LG08 substition matrice. The parameters names are @var{CodonProt.123_T92.kappa} and @var{CodonProt.beta}. @end table Optional words to describe the use of equilibrium frequencies sets. This word should be used with nucleotidic models which equilibrium distribution is fixed, ans does not depend on parameters. Otherwise there may be problems of identifiability of the parameters. @table @command @item Freq(frequencies=@{frequencies set description@}) Sustitution rates are multiplied by the frequency of the target codon in the given frequencies set. This factor is described by the @var{frequencies} argument. See the description of the Frequencies Set below. @cartouche @example alphabet=Codon(letter=DNA) genetic_code=Standard model=CodonDistFreq(frequencies=Full()) @end example @end cartouche has parameters @var{CodonDistFreq.012_T92.kappa}, @var{CodonDistFreq.Full.theta_1}, ..., @var{CodonDistFreq.Full.theta_60}, @var{CodonDistFreq.beta}. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1CodonDistanceFrequenciesSubstitutionModel.html#details, Bio++ description, Bio++ description}. @item PhasFreq(frequencies=@{frequencies set description@}) The sustitution rates are multiplied by the product of the frequencies of the changed nucleotides -- conditioned on the phase -- in the given frequencies set. This factor is described by the @var{frequencies} argument. See the description of the Frequencies Set below. For example, see the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1CodonDistancePhaseFrequenciesSubstitutionModel.html#details, Bio++ description, Bio++ description}. @end table In addition some models are defined that allow multiple substitions, with similar logic of included words. These models are prefixed by @var{Kron}. @table @command @item KronDistFreq(model=@{model name@} [,positions=pos1*pos2*...*posn + posx*...*posm + ...)]) @item KronDistFreq(model1=@{model name@}, model1=@{model name@}, ..., modeln=@{model name@}[,positions=pos1*pos2*...*posn + posx*...*posm + ...]) substitution model on codons as @var{CodonDistFreq} above, allowing simultaneous substitutions. Optional argument @var{positions} can be used to describe which substitutions are allowed. See model @xref{Kron}. @item KronDist(model=@{model name@} [,positions=pos1*pos2*...*posn + posx*...*posm + ...)]) @item KronDist(model1=@{model name@}, model1=@{model name@}, ..., modeln=@{model name@}[,positions=pos1*pos2*...*posn + posx*...*posm + ...]) substitution model on codons as @var{CodonDist} above, allowing simultaneous substitutions. Optional argument @var{positions} can be used to describe which substitutions are allowed. See model @xref{Kron}. @item KCM7() and KCM19() Kronecker Codon Model based on a unique (KCM7) or one per position (KCM19) GTR model. From Zaheri \& al, MBE, 2014. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1KCM.html#details, Bio++ description, Bio++ description}. @end table @node Multiple, Meta, Codon, Model @subsubsection General multiple site models @table @command @item Word(model=@{model name@} [,relrate1=@{1>real>0@}, ..., relrate@{n-1@}=@{1>real>0@}]) or @item Word(model1=@{model name@}, model1=@{model name@}, ..., modeln=@{model name@}[, relrate1=@{1> real>0@}, ..., relrate@{n-1@}=@{1> real>0@}]) substitution model on words. The arguments @var{model} and @var{model@{i@}} are for descriptions of models on single sites such as nucleotides or proteins. The alphabet must be a Word alphabet. If the argument is @var{model}, the length of the words in the substitution model is determined by the length of the words in the alphabet, and the @emph{same} single site model is used (ie the parameters are shared between all positions). If the arguments are @var{model1}, ..., @var{model@{n@}}, the length of the words in the alphabet must be @var{n}, and each single site model stands for a single-site substitution model. In that case, all single site models parameters are position dependent. Each single site model is normalized and the substitution rates between words that differ on more than one letter are null. Arguments @var{relrate@{i@}} stands for the relative substitution rates of the sites. Default: @var{relrate@{i@}=1/@{n-i+1@}}, such that the rate of each site is 1/n. @cartouche @example alphabet=Word(letter=DNA,length=4) model=Word(model=T92()) @end example @end cartouche builds a model on 4 bases words, such all sites follow the same T92 model. The parameters names are @var{Word.1234_T92.kappa}, @var{Word.relrate1}, @var{Word.relrate2}, @var{Word.relrate3}. @cartouche @example alphabet=Word(letter=DNA,length=4) model=Word(model1=T92(), model2=T92(), model3=JC69(), \ model4=HKY85()) @end example @end cartouche builds a model on 4 bases words, such first and second sites follow independent T92 models, third site follows a JC69 model, and fourth site follows a HKY85 model. Then the parameters names are @var{Word.1_T92.kappa}, @var{Word.2_T92.kappa}, @var{Word.4_HKY85.kappa}, @var{Word.4_HKY85.theta}, @var{Word.4_HKY85.theta1}, @var{Word.4_HKY85.theta2}, @var{Word.relrate1}, @var{Word.relrate2}, @var{Word.relrate3}. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1WordSubstitutionModel.html#details, Bio++ description, Bio++ description}. @item Kron(model=@{model name@} [,positions=pos1*pos2*...*posn + posx*...*posm + ...)]) @anchor{Kron} @item Kron(model1=@{model name@}, model1=@{model name@}, ..., modeln=@{model name@}[,positions=pos1*pos2*...*posn + posx*...*posm + ...]) substitution model on words, allowing simultaneous substitutions. The arguments @var{model} and @var{model@{i@}} are for descriptions of models on single sites such as nucleotides or proteins. The alphabet must be a Word alphabet. If the argument is @var{model}, the length of the words in the substitution model is determined by the length of the words in the alphabet, and the @emph{same} single site model is used (ie the parameters are shared between all positions). If the arguments are @var{model1}, ..., @var{model@{n@}}, the length of the words in the alphabet must be @var{n}, and each single site model stands for a single-site substitution model. In that case, all single site models parameters are position dependent. The rate of a multiple substitution is the product of the rates of the single substitutions it is made of. Without optional argument @var{positions}, all single and multiple substitutions are allowed. Optional argument @var{positions} describes the allowed substitutions. It is written as a formula with positions between 1 and the length of the word, and symbols '*' (to link positions that must change together) and '+' (to link sets of multiple susbtitutions that are allowed). As examples, on a DNA word with 3 positions: @cartouche @example model=Kron(model=K80(), positions=1*2*3) @end example @end cartouche allows only substitutions that change the 3 positions. @cartouche @example model=Kron(model=K80(), positions=1*2+3) @end example @end cartouche allows only substitutions that change the positions 1 and 2, and the ones that change position 3 alone. @cartouche @example model=Kron(model=K80(), positions=1*2+2*3) @end example @end cartouche allows only substitutions that change two neighbor positions. @cartouche @example model=Kron(model=K80(), positions=1+2+3) @end example @end cartouche allows only substitutions that change one position, i.e. @var{Word} model. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1KronSubstitutionModel.html#details, Bio++ description, Bio++ description}. @item Triplet(model=@{model description@} [, relrate1=@{real>0@}, relrate2=@{real>0@}]) or @item Triplet(model1=@{model description@}, model2=@{model description@}, model3=@{model description@}[, relrate1=@{real>0@}, relrate2=@{real>0@}]) substitution model on 3 letters words. The arguments @var{model} and @var{model@{i@}} are for descriptions of models on single sites such as nucleotides or proteins. The alphabet must be a 3-letters word alphabet or a codon alphabet. If the argument is @var{model}, the @emph{same} single site model is used on all positions (ie the parameters are shared between all positions). If the arguments are @var{model1}, @var{model2}, @var{model3}, each single site model stands for a single-site substitution model. In that case, all single site models parameters are position dependent. Each single site model is normalized and the substitution rates between triplets that differ on more than one letter are null. Arguments @var{relrate@{i@}} stands for the relative substitution rates of the sites. Default: @var{relrate@{i@}=1/@{4-i@}}, such that the rate of each site is 1/3. @cartouche @example alphabet=Codon(letter=DNA) genetic_code=Standard model=Triplet(model=T92) @end example @end cartouche builds a model on codons, such all sites follow the same T92 model. The parameters names are @var{Triplet.123_T92.kappa}, @var{Triplet.relrate1}, @var{Triplet.relrate2}. @cartouche @example alphabet=Word(letter=DNA, length=3) model=Triplet(model1=T92, model2=T92, model3=JC69) @end example @end cartouche builds a model on 3 bases words, such first and second sites follow independent T92 models, and third site follows a JC69 model. Then the parameters names are @var{Triplet.1_T92.kappa}, @var{Triplet.2_T92.kappa}, @var{Triplet.relrate1}, @var{Triplet.relrate2}. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1TripletSubstitutionModel.html#details, Bio++ description, Bio++ description}. @item YpR_Sym(model=@{model description@}, [rCgT=@{real>=0@}, rTgC=@{real>=0@}, rCaT=@{real>=0@}, rTaC=@{real>=0@}]) substitution model on quotiented triplets to handle strand symetric neighbour-dependency inside dinucleotides YpR (see Bérard and Guéguen 2012). See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1YpR_SymSubstitutionModel.html#details, Bio++ description, Bio++ description}. @item YpR_Gen(model=@{model description@}, [rCgT=@{real>=0@}, rcGA=@{real>=0@}, rTgC=@{real>=0@}, rtGA=@{real>=0@}, rCaT=@{real>=0@}, rcAG=@{real>=0@}, rTaC=@{real>=0@}, rtAG=@{real>=0@}]) substitution model on quotiented triplets to handle general symetric neighbour-dependency inside dinucleotides YpR (see Bérard and Guéguen 2012). See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1YpR_GenSubstitutionModel.html#details, Bio++ description, Bio++ description}. @end table @node Meta, Mixture, Multiple, Model @subsubsection Meta models These substitution models take as argument another substitution model, and add several parameters. @table @command @item TS98(model=@{model description@}, s1=@{real>0@}, s2=@{real>0@} [, "equilibrium frequencies"]) Tuffley and Steel 1998's 'covarion' model, taking a nested substitution model as argument for @var{model}. The nested model can be any substitution model for any alphabet. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1TS98.html#details, Bio++ description, Bio++ description}. @item G01(model=@{model description@}, rdist=@{rate distribution description@}, mu=@{real>0@} [, "equilibrium frequencies"]) Galtier 2001's 'covarion' model, taking a nested substitution model as argument for @var{model} and a rate distribution for parameter @var{rdist} (see below). The nested model can be any substitution model for any alphabet. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1G01.html#details, Bio++ description, Bio++ description}. @item RE08(model=@{model description@}, lambda=@{real>0@}, mu=@{real>0@} [, "equilibrium frequencies"]) Rivas and Eddy 2008's substitution model with gaps, taking a nested substitution model as argument for @var{model}. Parameter @var{lambda} is the insertion rate, while @var{mu} is the deletion rate. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1RE08.html#details, Bio++ description, Bio++ description}. @end table @node Mixture, Conditioned , Meta, Model @subsubsection Mixture of models @table @command Mixed models are sometimes called "site models". Mixed models combine substitution models with respective probabilities. We call submodels all the models that are mixed in the mixture. A Mixed model is either the mixture of several predefined models, or based on a "simple" model in which some parameters follow given distributions. During the likelihood computation process, all the submodels of the mixture are successively applied on the branches, and the mean (see below) of all the likelihoods is computed. A site can follow given paths all along the tree, with given probabilities. In homogeneous reconstruction, a path corresponds to a same submodel on all the branches, in a stationary condition. The probability of a path is the probability of its submodel. Given a site follows a path, a likelihood can be computed; and the overall likelihood on this site is the mean of these likelihoods (given the probabilities of the paths). This means that the root distribution is a mixture of the equilibrium distributions of the submodels. With nonhomogeneous reconstruction, several models are applied on the tree, some models are mixed, some are not. A path is a vector which size is the number of mixed models (see below for more details and the declaration of paths). Since the attribution of a submodel from a mixed model to a given site is a unique random variable, affecting the same mixed model to a set of branches S means that the attribution to this site is the same on all the branches of S. If model M=(Ma,Mb,Mc) is defined on a set of branches S, a site in constrained to follow either Ma on all S, or Mb on all S, or Ms on all S. If we want that two branches of S are independant, two similar mixed models must be defined. Moreover, it is possible to define paths that define dependencies between submodels of different mixtures (see below). @item MixedModel(model=@{model description@}) Mixture model from a given @var{model} in which some parameters follow a probabilistic distribution. Any discrete distribution available can be used @xref{Discrete distributions}. The description of the parameters distributions is described below. In case the range of a parameter is limited, the domain of the corresponding distribution is truncated accordingly. @cartouche @example model=MixedModel(model=TN93(kappa1=Gamma(n=4,alpha=3,beta=1),\ kappa2=Exponential(lambda=2),\ theta=0.5,theta1=0.2,theta2=0.1)) @end example @end cartouche has parameters @var{TN93.kappa1_Gamma.alpha}, @var{TN93.kappa1_Gamma.beta}, @var{TN93.kappa2_Exponential.lamba}, @var{TN93.theta}, @var{MixedModel.TN93.theta1}, @var{TN93.theta2}. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1MixtureOfASubstitutionModel.html#details, Bio++ description, Bio++ description}. @item Mixture(model1=@{model description@},..., modeln=@{model description@} [, relrate1=@{1>real>0@},..., relrate@{n-1@}=@{1>real>0@}, relproba1=@{1>real>0@}, ..., relproba@{n-1@}=@{1>real>0@}, "equilibrium frequencies"]) Mixture model built from several @var{models}: each model has its own probability and rate. Arguments @var{relproba@{i@}} stands for the relative probability and @var{relrate@{i@}} stands for the relative rate of each model (in the order the models are given). Default: @var{relproba@{i@}=1/@{n-i+1@}}, such that the probabilty of each site is 1/n, and @var{relrate@{i@}=1/@{n-i+1@}} such that the rate of each site is 1. @cartouche @example model=Mixture(model1=GY94(), model2=YN98(), relrate1=0.1) @end example @end cartouche has parameters@var{Mixture.relrate1}, @var{Mixture.relproba1}, @var{Mixture.1_GY94.kappa}, @var{Mixture.1_GY94.V}, @var{Mixture.2_YN98.kappa}, @var{Mixture.2_YN98.omega}. See the @uref{http://bioweb.me/bpp-phyl-doc/classbpp_1_1MixtureOfSubstitutionModels.html#details, Bio++ description, Bio++ description}. @end table @node Conditioned, , Mixture, Model @subsubsection Conditioned models The transition probabilities on the branches are conditioned by the occurence of given events. The model is then no-markovian, but semi-markovian. The sets of considered events follow the one (ie register) defined for substitution mapping (see the testnh manual). @table @command @item OneChange(model=@{model description@}) The transition probabilities along each branch are conditioned by the fact that there has been at least one substitution on this branch with thid model. @item OneChange(model=@{model description@}, register=@{register name@}, numReg=num1+num2+...) The transition probabilities along each branch are conditioned by the fact that there has been on this branch at least one substitution of the specific types in the register. The "+" permits the declaration of several types. @end table @node Non-homogeneity, FrequenciesSet, Model, Process @subsection Setting up non-stationary / non-homogeneous models You can specify a wide range of non-homogeneous models, by combining different options. @subsubsection One-per-branch non-homogeneous models This option share the same parameters as the homogeneous case, since the same kind of model is used for each branch. The additional options are the following: @table @command @item nonhomogeneous_one_per_branch.shared_parameters = @{list@} List the names of the parameters that are shared by all branches. In Galtier & Gouy model, that would be @var{T92.kappa}, since only the theta parameter is branch-specific. The '*' wildcard can be used, as in @command{*theta*} for all the parameters whose name has @command{theta} in it. @end table @subsubsection General non-homogeneous models Bio++ provides a general syntax to specify almost any non-homogeneous model. @table @command @item nonhomogeneous.number_of_models = @{int>0@} Set the number of distinct models to use. @end table You now have to configure each model individually, using the syntax introduced for the homogeneous case, excepted that model will be numbered, for instance: @cartouche @example model1 = T92(theta=0.39, kappa=2.79) @end example @end cartouche The additional option is available to attach the model to branches in the tree, specified by the id of the upper node in the tree: @table @command @item model1.nodes_id = 1,5,10:15,19 Specify the ids of the nodes to which the node is attached. Id ranges can be specified using the @option{begin:end} syntax. @end table Finally, you may find useful the following options: @table @command @item output.parameter_names.file = @{@{path@}|none@} A text file listing all parameter names. This might come handy in order to specify the parameter that should not be optimized (see optimization.ignore_parameter) or aliased (see above). The use of that option will cause the program to exit just after producing the list file. @end table @subsubsection Paths among non-homogeneous mixture models To define constraints for sites between submodels, we can set "paths" that any site must follow. For example, in the following description: @cartouche @example nonhomogeneous = general nonhomogeneous.number_of_models = 3 model1=T92() model2=MixedModel(model=T92(kappa=Simple(values=(4,10,20),\ probas=(0.1,0.5,0.4)))) model3=MixedModel(model=TN93(theta1=Simple(values=(0.1,0.5,0.9),\ probas=(0.3,0.2,0.5)))) model1.nodes_id=0:1 model2.nodes_id=2:3 model3.nodes_id=4:5 @end example @end cartouche In this case, on branches 2 & 3 a site follows any submodel of model 2 (but the same submodel on both branches), and on branches 4 & 5, a site follows any submodel of model 3 (the same on both branches as well). But there is no constraint between models 2 & 3, which means that a site can follow any submodel of model 2 and any submodel of model 3. If the user wants that a site with @var{T92.kappa=4} in model 2 has @var{TN93.theta1=0.1} in model 3, that a site with @var{T92.kappa=10} in model 2 has @var{TN93.theta1=0.9} in model 3, and that other cases are free (in this case it means that @var{T92.kappa=20} in model 2 is linked with @var{TN93.theta1=0.5} in model 3), then we can use the declarations: @cartouche @example site.number_of_paths=2 site.path1=model2[T92.kappa_1] & model3[TN93.theta1_2] site.path2=model2[T92.kappa_2] & model3[TN93.theta1_3] @end example @end cartouche The third path (for the remaining submodels) is automatically computed. It is possible to link mixtures of submodels. For example, @cartouche @example site.path1=model2[T92.kappa_1] & model3[TN93.theta1_2]\ & model3[TN93.theta1_3] @end example @end cartouche means that a site that has @var{T92.kappa=4} in model2 has either @var{TN93.theta1=0.5} or @var{TN93.theta1=0.9} in model3. Because of these constraints, the probabilities of the submodels are linked. In the first example, probability of @var{T92.kappa=4} in model 2 equals the probability of @var{TN93.theta1=0.5} in model 3. Since it is contradictory with the probabilities defined in models 2 or 3, the reference probabilities are the ones of the first numbered mixed model, here model 2. In this case, the probabilities in model 3 may have no use, but with the second example the probability of submodel T92.kappa=4 equals the sum of the probabilities of submodels TN93.theta1=0.5 or TN93.theta1=0.9. The relative proportion of those models used in the declaration of model 3 is then used. Here their respective probabilities are then: 0.1*0.2/ (0.2+0.5)=0.0286 and 0.1*0.5/(0.2+0.5)=0.0714. Concerning the optimization procedure, this choice may entail the non- identifiability of several parameters (here the probabilities in model 3), so the user should be careful about this. When the submodel is aliased behind a model name, the paths should be defined as combinations of the model that is mixed. For example, YNGP_M2 is made of 3 YN98 models, depending of three @var{omega} values: <1, =1, >1. If we want a site to switch between <1 and >1 omega values between two sets of branches: @cartouche @example nonhomogeneous = general nonhomogeneous.number_of_models = 2 model1=YNGP_M2(frequencies=F1X4) model2=YNGP_M2(frequencies=F1X4) model1.nodes_id=0:1 model2.nodes_id=2:3 site.number_of_paths=3 site.path1=model1[YN98.omega_1] & model2[YN98.omega_3] site.path2=model1[YN98.omega_2] & model2[YN98.omega_2] site.path3=model1[YN98.omega_3] & model2[YN98.omega_1] @end example @end cartouche Another example in the case of mixtures of mixed models, where the submodels are defined by their names: @cartouche @example nonhomogeneous = general nonhomogeneous.number_of_models = 2 model1=LLG08_UL2() model2=LLG08_UL3() site.number_of_paths=2 site.path1=model1[LLG08_UL2.M2] & model2[LLG08_UL3.Q1] site.path2=model1[LLG08_UL2.M1] & model2[LLG08_UL3.Q2] \ & model2[LLG08_UL3.Q3] @end example @end cartouche When nonhomogeneity option is @option{one_per_branch}, each site is constrained to follow the same submodel from leaves to root. @subsubsection Root frequencies In case of nonstationary models, the ancestral frequencies are distinct parameters. If a model is assumed to be stationary, the ``None'' parameter value can be used, which is strictly equivalent to setting @command{nonhomogeneous.stationary=yes}. When the model is a mixture model, since there is not a set of equilibrium frequencies, with this option the root frequencies are set to be the average (with the respective probabilities of the submodels) of the equilibrium frequencies of the submodels. As since version 0.4.0, BppSuite uses the keyval syntax to set up root frequencies, @table @command @item nonhomogeneous.root_freq=@{frequency set description@} @end table The Frequencies set used can be any of the ones described below @xref{Frequencies sets}, depending on the alphabet used. @node FrequenciesSet, Rates, Non-homogeneity, Process @subsection Frequencies sets @anchor{Frequencies sets} The following frequencies distributions are available: @table @command @item Fixed() All frequencies are fixed to their initial value and are not estimated. @item GC(theta=@{real]0,1[@}) For nucleotides only, set the G content equal to the C content. @item Full(theta1=@{real]0,1[@}, theta2=@{real]0,1[@}, ..., thetaN=@{real]0,1[@}) Full parametrization. Contains N free parameters, where N is equal to the size of the alphabet - 1. For codon models, N is the size of the alphabet - 1 - the number of stop codons, whose frequencies are set to 0. For nucleotide sequences, theta is the GC content, theta1 is the proportion of A over A+T, and theta2 is the proportion of G over G+C. @item Empirical(file=@{path@} [,col=@{int@}]) Read frequencies from a file. Each frequencies is set as plain column in the file. If several columns are in the file, the number of the column can be given with @{col@} argument (default: 1). @item Empirical+F(name=@{chars@}, file=@{path@}, [theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@}, ..., "equilibrium frequencies"]) Build a protein substitution model from a file in PAML format, and use free equilibrium frequencies. 'name' will be used as a parameter namespace, including for frequencies. @item Word(frequency=@{frequency set description@}) or @item Word(frequency1=@{frequency set description@}, frequency2=@{frequency set description@}, ..., frequencyn=@{frequency set description@}) frequencies on words computed as the product of frequencies on the letters. The arguments @var{frequency} and @var{frequency@{i@}} are for descriptions of frequency sets on single sites such as nucleotides or proteins. The alphabet must be a Word alphabet. If the argument is @var{frequency}, the number of multiplied single site frequencies is the length of the words in the alphabet, and the @emph{same} single site frequency set is used (ie the parameters are shared between all positions). If the arguments are @var{frequency1}, ..., @var{frequency@{n@}}, the length of the words in the alphabet must be @var{n}, and all single site frequency sets are independent. In that case, all single site frequency set parameters are position dependent. @cartouche @example alphabet=Word(letter=DNA,length=4) nonhomogeneous.root_freq=Word(frequency=GC()) @end example @end cartouche builds a root frequency set on 4 bases words, such that all sites frequencies follow the same GC frequency set model. The parameter name is @var{1234_GC.theta}. @cartouche @example alphabet=Word(letter=DNA,length=4) nonhomogeneous.root_freq=Word(frequency1=GC(),frequency2=GC(),\ frequency3=Fixed(),frequency4=Full()) @end example @end cartouche builds a root frequency set on 4 bases words, such first and second sites follow independent GC frequency sets, third site follows a Fixed frequency set, and fourth site follows a Full frequency set. Then the parameters names are @var{1_GC.theta}, @var{2_GC.theta}, @var{4_Full.theta_1}, @var{4_Full.theta_2}, @var{4_Full.theta_3}. @item Codon(frequency=@{frequency set description@}) or @item Codon(frequency1=@{frequency set description@}, frequency2=@{frequency set description@}, frequency3=@{frequency set description@}) frequencies on codons computed as the product of frequencies on the letters, with stop codon frequencies set to zero. The arguments @var{frequency} and @var{frequency@{i@}} are for descriptions of frequency sets on nucleotides. The alphabet must be a Codon alphabet. If the argument is @var{frequency}, the @emph{same} single site frequency set is used (ie the parameters are shared between all positions). If the arguments are @var{frequency1}, @var{frequency2}, @var{frequency3}, all single site frequency sets are independent. In that case, all single site frequency set parameters are position dependent. @cartouche @example alphabet=Codon(letter=DNA) genetic_code=Standard nonhomogeneous.root_freq=Codon(frequency=GC()) @end example @end cartouche builds a frequency set on codons, such that all sites frequencies follow the same GC frequency set model. The parameter name is @var{123_GC.theta}. @cartouche @example alphabet=Codon(letter=DNA) genetic_code=Standard nonhomogeneous.root_freq=Codon(frequency1=GC(),frequency2=GC(),\ frequency3=Fixed()) @end example @end cartouche builds a frequency set on codons, such that first and second sites follow independent GC frequency sets, third site follows a Fixed frequency set. Then the parameters names are @var{1_GC.theta}, @var{2_GC.theta}. Predefined codon frequencies are available, with a syntax similar to the one used in the PAML software. See above Codon Models section. @end table All functions accept the following arguments, that take priority over the parameter specification: @table @command @item init=@{balanced,observed@} Set all frequencies to the same value, or to their observed counts. @item observedPseudoCount=@{integer@} If the frequencies are set from observed counts, a pseudoCount is added to all the counts. @item values=(@{vector@}) Explicitly set all frequencies manually. The size of the input vector should equal the number of resolved states in the alphabet, be in alphabetical order of states, and sum to one. @end table @node Rates, Linking, FrequenciesSet, Process @subsection Rate across site distribution @table @command @item rate_distribution = @{rate distribution description@} Specify the rate across sites distribution. @end table The rate distribution is set to have a mean of 1. The following distributions are currently available: @table @command @item Constant Uses a constant rate across sites. @item Gamma(n=@{int>=2@}, alpha=@{float>0@}) A discretized gamma distribution of rates, with @var{n} classes, and a given shape, with mean 1 (scale=shape). @item Invariant(dist=@{rate distribution description@}, p=@{real[0,1]@}) A composite distribution allowing a special class of invariant site, with a probability @var{p}. @end table @node Linking, , Rates, Process @subsection Linking parameters It is possible to reduce the parameter space by putting extra constraints on parameters, using for instance @cartouche @example model=TN93(kappa1=1.0, kappa2=kappa1, theta=0.5) @end example @end cartouche In that particular case the resulting model is strictly equivalent to the HKY85 model. This syntax however allows to define a larger set of models. As long as their range match, parameters of several objects (models, root frequencies, rates, etc) can be linked. For instance: @cartouche @example model1 = T92(theta=GC.theta, kappa=3) model2 = T92(theta=0.39, kappa=T92.kappa_1) nonhomogeneous.root_freq=GC @end example @end cartouche In the case of nonhomogeneous modelling, a specific syntax is available: @cartouche @example nonhomogeneous.alias = @{list of aliases@} @end example @end cartouche where each alias is described as `param1->param2'. The full name of the parameters have to be used, see for example: @cartouche @example model1 = T92(theta=0.4, kappa=4) model2 = GTR(theta=0.4, a = 1.1, b=0.4, c=0.4, d=0.25, e=0.1) nonhomogeneous.alias=GTR.theta1->T92.theta1 @end example @end cartouche This option can be used to link parameters of the root frequencies if the model is non-stationary: @cartouche @example model1=GTR(theta1=0.7) nonhomogeneous.root_freq=Full(init=balanced) nonhomogeneous.alias=Full.theta1->GTR.theta1_1 @end example @end cartouche Note that this option is only available with the 'general' nonhomogeneous substitution models and will be ignored if used with "one_per_branch". @node Distribution, Estimation, Process, Common @section Discrete distributions @anchor{Discrete distributions} Bio++ contains several probability distributions (currently only dicrete or discretized ones). These are: @subsection Standard Distributions @table @command @item Constant(value=@{float@}) a Dirac distribution on @var{value}, with parameter @var{value}. @item Beta(n=@{int>=2@}, alpha=@{float>0@}, beta=@{float>0@}) a discretized beta distribution, with @var{n} classes, with standard parameters @var{alpha} and @var{beta}. @item Gamma(n=@{int>=2@}, alpha=@{float>0@}, beta=@{float>0@}) a discretized gamma distribution, with @var{n} classes, a shape @var{alpha} and a rate @var{beta}, with parameters @var{alpha} and @var{beta}. @item Gaussian(n=@{int>=1@}, mu=@{float@}, sigma=@{float>0@}) a discretized gaussian distribution, with @var{n} classes, a mean @var{mu} and a standard deviation @var{sigma}, with parameters @var{mu} and @var{sigma}. @item Exponential(n=@{int>=2@}, lambda=@{float>0@}) a discretized exponential distribution, with @var{n} classes and parameter @var{lambda}. @item Simple(values=@{vector@}, probas=@{vector@} [, ranges=@{vector@}]) a discrete distribution with specific values (in @var{values}) and their respective non-negative probabibilities (in @var{probas}). The parameters are @var{V1}, @var{V2}, ..., @var{Vn} for all the values and the relative probabibility parameters are @var{theta1}, @var{theta2}, ..., @var{thetan-1}. Optional argument @{ranges@} sets the allowed ranges of values taken by the parameters; usage is like @samp{ranges=(V1[0.2;0.9],V2[1.1;999])}. @item TruncExponential(n=@{int>=2@}, lambda=@{float>0@}, tp=@{float>0@}) a discretized truncated exponential distribution, with @var{n} classes, parameter @var{lambda} and a truncation point @var{tp}. The parameters are @var{lambda} and @var{tp}. @item Uniform(n=@{int>=1@}, begin=@{float>0@}, end=@{float>0@}) a uniform distribution, with @var{n} classes in interval [@var{begin},@var{end}]. There are no parameters. @end table @subsection Mixture Distributions @table @command @item Invariant(dist=@{distribution description@}, p=@{float>0@}) a Mixture of a given discrete distributution and a 0 Dirac. @var{p} is the probability of this 0 Dirac. For example : @cartouche @example Invariant(dist=Gaussian(n=4,2,0.5),p=0.1) @end example @end cartouche builds a mixture of a gaussian distribution with 4 categories (and probability 0.9) and a 0 Dirac with probability 0.1. Overall, there are 5 categories. The parameters names are @var{Invariant.Gaussian.mu}, @var{Invariant.Gaussian.sigma}, @var{Invariant.p}. @item Mixture(probas=@{vector@}, dist1=@{distribution description@}, ..., distn=@{distribution description@}) a Mixture of discrete distributions with specific probabilities (in @var{probas}) and their respective desccriptions (in @var{probas}). The parameters are the relative probabibility parameters @var{theta1}, @var{theta2}, ..., @var{thetan-1}, and the parameters of the included distributions prefixed by @var{Mixture.i_} where @var{i} is the order of the distribution. For example: @cartouche @example Mixture(probas=(0.3,0.7),dist1=Beta(n=5,alpha=2,beta=3),\ dist2=Gamma(n=10,alpha=9,beta=2)) @end example @end cartouche builds a mixture of a discrete beta distribution and of a discrete gamma distribution, with a total of 15 classes. The parameters names are @var{Mixture.theta1}, @var{Mixture.1_Beta.alpha}, @var{Mixture.1_Beta.beta}, @var{Mixture.2_Gamma.alpha} and @var{Mixture.2_Gamma.beta}. @end table @c ------------------------------------------------------------------------------------------------------------------ @node Estimation, WritingSequences, Distribution, Common @section Numerical parameters estimation Some programs allow you to (re-)estimate numerical parameters, including @itemize @bullet @item Branch lengths @item Entries of the substitution matrices, included base frequencies values) @item Parameters of the rate distribution (currently shape parameter of the gamma law, proportion of invariant sites). @end itemize @table @command @item optimization = @{method@} where ``method'' can be one of @table @command @item None No optimization is performed, initial values are kept ``as is''. @item FullD(derivatives=@{Newton|Gradient@}) Full-derivatives method. Branch length derivatives are computed analytically, others numerically. The @var{derivatives} arguments specifies if first or second order derivatives should be used. In the first case, the optimization method used is the so-called conjugate gradient method, otherwise the Newton-Raphson method will be used. @item D-Brent(derivatives=@{Newton|Gradient@}, nstep=@{int>0@}) Branch lengths parameters are optimized using either the conjugate gradient or the Newton-Raphson method, other parameters are estimated using the Brent method in one dimension. The algorithm then loops over all parameters until convergence. The @var{nstep} arguments allow to specify a number of progressive steps to perform during optimization. If @option{nstep=3} and @option{precision=E-6}, a first optimization with @option{precision=E-2}, will be performed, then a round with @option{precision} set to E-4 and finally @option{precision} will be set to E-6. This approach generally increases convergence time. @item D-BFGS(derivatives=@{Newton|Gradient@}, nstep=@{int>0@}) Branch lengths parameters are optimized using either the conjugate gradient or the Newton-Raphson method, other parameters are estimated using the BFGS method. The algorithm then loops over all parameters until convergence. The @var{nstep} arguments allow to specify a number of progressive steps to perform during optimization. If @option{nstep=3} and @option{precision=E-6}, a first optimization with @option{precision=E-2}, will be performed, then a round with @option{precision} set to E-4 and finally @option{precision} will be set to E-6. This approach generally increases convergence time. @end table @item optimization.reparametrization = @{boolean@} Tells if parameters should be transformed in order to remove constraints (for instance positivie-only parameters will be log transformed in order to obtain parameters defined from -inf to +inf). This may improve the optimization, particularly for parameter-rich models, but the likelihood calculations will take a bit more time. @item optimization.final = @{powell|simplex@} Optional final optimization step, useful if numerical derivatives are to be used. Leave the field empty in order to skip this step. @item optimization.profiler = @{@{path@}|std|none@} A file where to dump optimization steps (a file path or std for standard output or none for no output). @item optimization.message_handler = @{@{path@}|std|none@} A file where to dump warning messages. @item optimization.max_number_f_eval = @{int<0@} The maximum number of likelihood evaluations to perform. @item optimization.ignore_parameter = @{list@} A list of parameters to ignore during the estimation process. The parameter name should include there "namespace", that is their model name, for instance K80.kappa, TN93.theta, GTR.a, Gamma.alpha, etc. For nested models, the syntax is the following: @command{G01.rdist_Gamma.alpha}, @command{TS98.model_T92.kappa}, @command{RE08.lamba}, @command{RE08.model_G01.model_GTR.a}, etc. 'Ancient' will ignore all parameters in the ancestral frequency set (non-homogeneous models), 'BrLen' will ignore all branch lengths and 'Model' will ignore all model parameters. The '*' wildcard can be used, as in @command{*theta*} for all the parameters whose name has @command{theta} in it. @item optimization.constrain_parameter = @{list@} A list of parameters on which the authorized values are limited to a given interval. @cartouche @example optimization.constrain_parameter = YN98.omega = [-inf;1.9[,\ *theta* = [0.1;0.7[, BrLen*=[0.01;inf] @end example @end cartouche @item optimization.tolerance = @{float>0@} The precision on the log-likelihood to reach. @item output.infos = @{@{path@}|none@} A text file containing several statistics for each site in the alignment. These statistics include the posterior rate, rate class with maximum posterior probability and whether the site is conserved or not. @end table The resulting tree will be written to a file specified by the general tree writing options (@ref{WritingTrees}). @c ------------------------------------------------------------------------------------------------------------------ @node WritingSequences, WritingTrees, Estimation, Common @section Writing sequences/alignments to files @table @command @item output.sequence.file = @{path@} The output file where to write the sequences. @item output.sequence.format = @{sequence format description@} The output file format, using the same syntax as for reading (@pxref{Sequences}). Only formats Fasta, Mase and Phylip are supported for writing. In addition, most of the formats support the @command{length} argument, that specifies the maximum number of sequence characters to output on each line (default set to 100). @end table @c ------------------------------------------------------------------------------------------------------------------ @node WritingTrees, , WritingSequences, Common @section Writing trees to files @table @command @item output.tree.file = @{path@} The phylogenetic tree file to write to. @item output.tree.format = @{Newick|Nexus|NHX@} The format of the output tree file. @end table Some programs may require that you write multiple trees to a file. The corresponding options are then: @table @command @item output.trees.file = @{path@} The file that will contain multiple trees. @item output.trees.format = @{Newick|Nexus|NHX@} The format of the output tree file. @end table @c ------------------------------------------------------------------------------------------------------------------ @node Reference, , Common, Top @chapter Bio++ Program Suite Reference @c ------------------------------------------------------------------------------------------------------------------ This section now details the specific options for each program in the Bio++ Program suite. @c ------------------------------------------------------------------------------------------------------------------ @menu * bppml:: Bio++ Maximum Likelihood. * bppseqgen:: Bio++ Sequence Generator. * bppancestor:: Bio++ Ancestral Sequences and Rates reconstruction. * bppmixedlikelihoods:: Bio++ Site-Likelihoods Inside Mixed Models. * bppdist:: Bio++ Distance Methods. * bpppars:: Bio++ Maximum Parsimony. * bppconsense:: Bio++ Consensus Trees. * bppreroot:: Bio++ Serial Tree Re-rooting. * bppseqman:: Bio++ Sequences Manipulation. * bppalnscore:: Bio++ Alignment Scoring. * bpppopstats:: Bio++ Population Genetics Statistics. * bpptreedraw:: Bio++ Tree Drawing. @end menu @node bppml, bppseqgen, Reference, Reference @section BppML: Bio++ Maximum Likelihood The BppML program uses the common syntax introduced in the previous section for setting the alphabet, loading the sequences (@pxref{Sequences}), specifying the model (@pxref{Model}), and estimating parameters (@pxref{Estimation}). The BppML program allows you to optimize tree topologies and model parameters and perform a bootstrap analysis. @subsection Branch lengths initial values @table @command @item init.tree = @{user|random@} Set the method for the initial tree to use. The @option{user} option allows you to use an existing file using the method described in the Common options section. This file may have been built using another method like neighbor joining or parsimony for instance. The @option{random} option picks a random tree, which is handy to test convergence. This may however slows down significantly the optimization process. @item init.brlen.method = @{method description@} Set how to initialize the branch lengths. Available methods include: @table @command @item Input(midpoint_root_branch=@{boolean@}) Keep initial branch lengths as is. Additional argument specifies if the root position should be moved to the midpoint position of the branch containing it. @item Equal(value=@{float>0@}) Set all branch lengths to the same value, provided as argumemt. @item Clock Coerce to a clock tree. @item Grafen(height=@{@{real>0@}|input@}, rho = @{real>0@}) Uses Grafen's method to compute branch lengths. In Grafen's method, each node is given a weight equal to the number of underlying leaves. The length of each branch is then computed as the difference of the weights of the connected nodes, and further divided by the number of leaves in the tree. The height of all nodes are then raised to the power of 'rho', a user specified value. The tree is finally scaled to match a given total height, which can be the original one (@option{height=input}), or fixed to a certain value (usually @option{height=1}). A value of rho=0 provides a star tree, and the greater the value of rho, the more recent the inner nodes. @end table @item input.tree.check_root = @{boolean@} Tell if the input tree should be checked regarding to the presence of a root. If set to yes (the default), rooted trees will be unrooted if a homogenous model is used. If not, a rooted tree will be fitted, which can lead to optimization issues in most cases. Use the non default option with care! @end table @subsection Topology optimization @table @command @item optimization.topology = @{boolean@} Enable the tree topology estimation. @item optimization.topology.algorithm = @{NNI@} Algorithm to use for topology estimation: only NNI available for now. @item optimization.topology.algorithm_nni.method = @{fast|better|phyml@} Set the NNI method to use. @option{fast}: test sequentially all NNI, if a NNI improving the likelihood is found, it is performed. @option{better}: test all possible NNIs, do the one with the biggest likelihood increase. @option{phyml}: test all possible NNIs, try doing all the improving ones. If the final likelihoods is better, perform all NNIs. Otherwise, try to do half of them, and so on. In most cases the @option{phyml} option shows the best performance. @item optimization.topology.nstep = @{int>0@} Number of phyml topology movement steps before re-optimizing parameters. @item optimization.topology.numfirst = @{boolean@} Shall we estimate parameters before looking for topology movements? @item optimization.topology.tolerance.before = @{real>0@} Tolerance for the prior-topology estimation. The tolerance numbers should not be too low, in order to save computation time and also for a better topology estimation. The @option{optimization.tolerance} parameter will be used for the final optimization of numerical parameters (see Common options). @item optimization.topology.tolerance.during = 100 Tolerance for the during-topology estimation @item optimization.scale_first = no Shall we first scale the tree before optimizing parameters? @item optimization.scale_first.tolerance = @{double@} The convergence criterion to achieve in the optimization. @end table @subsection Molecular clock BppML can also optimize branch lengths with a molecular clock: @table @command @item optimization.clock=@{no|global@} Tell if a molecular clock should be assumed. Topology estimation is not possible with a clock constraint. @end table @subsection Output results @table @command @item output.infos = @{@{path@}|none@} Alignment information log file (site specific rates, etc): @item output.estimates = @{@{path@}|none@} Write parameter estimated values. @item output.estimates.alias = @{boolean@} Write the alias names of the aliased parameters instead of their values (default: true). @end table @subsection Bootstrap analysis @table @command @item bootstrap.number = @{int>0@} Number of replicates. A reasonable value would be >= 100. @item bootstrap.approximate = @{boolean@} Tell if numerical parameters should be kept to their initial value when bootstrapping. @item bootstrap.verbose = @{boolean@} Set this to yes for detailed output when bootstrapping. @item bootstrap.output.file = @{@{path@}|none@} Where to write the resulting trees (multi-trees newick format). @end table @subsection Rather technical options Theses options are mainly for debugging or testing purpose, in most case you will be happy with the default setting. @table @command @item likelihood.recursion = @{simple|double@} Set the type of likelihood recursion to use. @option{simple}: derivatives take more time to compute, but likelihood computation is faster. For big data sets, it can save a lot of memory usage too, particularly when the data are compressed. @option{double}: uses more memory and need more time to compute likelihood, due to the double recursion. Analytical derivatives are however faster to compute. This command has no effect in the following cases: (i) topology estimation: this requires a double recursive algorithm, (ii) optimization with a molecular clock: a simple recursion with data compression is used in this case, due to the impossibility of computing analytical derivatives. @item likelihood.recursion_simple.compression = @{simple|recursive@} Site compression for the simple recursion: @option{simple}: identical sites are not computed twice, @option{recursive}: look for site patterns to save computation time during optimization, but requires extra time for building the patterns. This is usually the best option, particularly for nucleotide data sets. @end table @c ------------------------------------------------------------------------------------------------------------------ @node bppseqgen, bppancestor, bppml, Reference @section BppSeqGen: Bio++ Sequence Simulator The BppSeqGen program uses the common syntax introduced in the previous section for setting the alphabet, loading the sequences (@pxref{Sequences}) and tree (@pxref{Tree}), specifying the model (@pxref{Model}) and writing sequence data (@pxref{WritingSequences}). The root sequence can be sampled from the model specification, with additional argument: @table @command @item number_of_sites = @{int>0@} The number of site positions to simulate. @end table Or the root sequence can be built from a file of a sequence: @table @command @item input.sequence.file=@{path@} A sequence is be loaded, from which the simulation will be performed, or from which a root sequence can be sampled. (@pxref{Sequences}). @item input.infos = @{path@} A info file like the one output by bppML. The estimated site-specific rates will then be used to simulate the same number of sites as found in the info file, with the corresponding rates. In this case, additional options are possible: @table @command @item input.infos.rates = @{string@} Name of the column on which the rates are described (default: pr). @item input.infos.states = @{string@} Name of the column on which the states are read (default: none, which means a random sequence). @item input.site.selection = @{string@} used to sample from the given sequence (@pxref{Sequences}). @end table Addition optional arguments include: @table @command @item input.tree.scale = @{float@} An optional scaling factor for the branch length (default to 1.0) @item input.tree.method = @{single|MS|CoaSim@} Format of input tree(s). By default, a single tree is expected ('single'). Ancestral recombination graphs (ARGs), in the form of multiple trees, can also be provided in the MS or CoaSim format. Note that in the case of MS, ARG are given for a certain number of sites, wich should be provided as additional argument (e.g. @command{MS(number_of_sites=100)}). The ARG will be unscaled according to the given size, and rescaled according to the given number of sites to simulate. ARG in CoaSim format are already in relative scale. @end table In addition, command line argument @option{--seed=@{int>0@}} can be used to set the seed of the random generator. @end table @c ------------------------------------------------------------------------------------------------------------------ @node bppancestor, bppmixedlikelihoods, bppseqgen, Reference @section BppAncestor: Bio++ Ancestral Sequence and Rate Reconstruction The BppAncestor program uses the common syntax introduced in the previous section for setting the alphabet, loading the sequences (@pxref{Sequences}) and tree (@pxref{Tree}), specifying the model (@pxref{Model}) and writing sequence data (@pxref{WritingSequences}). Specific options are: @table @command @item input.tree.check_root = @{boolean@} Tell if the input tree should be checked regarding to the presence of a root. If set to yes (the default), rooted trees will be unrooted if a homogenous model is used. If not, a rooted tree will be fitted, which can lead to optimization issues in most cases. Use the non default option with care! @item asr.method = @{none|marginal@} Marginal is the only option for now. If set to "none", only nodes frequencies can be output. @item asr.probabilities = @{boolean@} Tells if we should output the site specific probabilities in each case. @item asr.sample = @{boolean@} Tell if we should sample from the posterior distribution instead of using the maximum probability. @item asr.sample.number = 10 [[asr.sample=yes]] Number of sample sequences to output. @item asr.add_extant = @{boolean@} Should extant (observed) sequences be added to the output sequence file? The sequences added are the ones which are used for the actual calculation. It they contained gaps for instance, and that these have been replaced by the unknown character (N or X for example), then the sequence with unknown characters will be used. @item output.sites.file = @{@{path@}|none@} Alignment information log file (site specific rates, probabilities, etc). @item output.nodes.file = @{@{path@}|none@} Ancestral nodes information: expected frequencies (prefix exp) (see Galtier & Gouy 1998) and a posteriori probabilities of ancestral states (prefix eb). @item output.nodes.add_extant = @{boolean@} Tell if leaf nodes should be added to the output file. @end table @c ------------------------------------------------------------------------------------------------------------------ @node bppmixedlikelihoods, bppdist, bppancestor, Reference @section BppMixedLikelihoods: Bio++ Site-Likelihoods Inside Mixed Models. The BppMixedLikelihoods program uses the common syntax introduced in the previous section for setting the alphabet, loading the sequences (@pxref{Sequences}) and tree (@pxref{Tree}) and specifying the model (@pxref{Model}). Given a mixed parameter name of mixed model, or a mixed model made of several models, the BppMixedLikelihoods program computes site per site log-likelihoods of the several values of the parameter, or of the several sub-models of the mixture. If the mixed model is built on a parameter which value follows a distribution, and in an additional column -- named "mean" -- the a posteriori mean value of the paramater is computed. Specific options are: @table @command @item output.likelihoods.file = @{@{path@}@} Ouput file of the program (site specific log-likelihood, and mean of the mixed parameters, if any). @item likelihoods.model_number = @{integer@} In case of a non-homogeneous modeling, the number of the mixed model which parameter or sub-models are considered. @item likelihoods.parameter_name = @{string@} If the considered mixed model is built from a distribution on a parameter, the name of the parameter to be considered. In this case, an additional column is written, in which the average a posteriori value of the parameter is. @end table @c ------------------------------------------------------------------------------------------------------------------ @node bppdist, bpppars, bppmixedlikelihoods, Reference @section BppDist: Bio++ Distance Methods The BppDist program uses the common syntax introduced in the previous section for setting the alphabet, loading the sequences (@pxref{Sequences}) and tree (@pxref{Tree}) and specifying the model (@pxref{Model}, only the section corresponding to the homogeneous case). Specific options are: @table @command @item output.matrix.file = @{@{path@}|none@} Where to write the matrix file (only philip format supported for now). @item method = @{wpgma|upgma|nj|bionj@} The algorithm to use to build the tree. @item optimization.method = @{init|pairwise|iterations@} There are several ways to optimize substitution parameters. The @option{init} option corresponds to the standard behavior, that is, keeping them to their initial, user-provided value. The @option{pairwise} option estimate those parameters in a pairwise manner. This should be avoided, particularly with parameter-rich models. Finally the @option{iterations} option corresponds to Ninio et al, Bioinformatics (2007) recursive algorithm: After each distance tree, a global ML estimation of the substitution parameters is performed. The estimated values are then used to rebuild a distance matrix and a tree. The algorithm stops when the topology does not change anymore. The ML optimization uses the parameters described in (@pxref{Estimation}). @item output.tree.file = @{@{path@}|none@} The final tree, possibly with bootstrap values: BppDist uses the same options for bootstrap analysis than the BppML program (@pxref{bppml}). @end table @c ------------------------------------------------------------------------------------------------------------------ @node bpppars, bppconsense, bppdist, Reference @section BppPars: Bio++ Maximum Parsimony The BppPars program is currently quite limited and should not be used for serious phylogenetic analysis. It can compute parsimony scores and perform topology estimation using the same algorithm of BppML. It uses the common syntax introduced in the previous section for setting the alphabet, loading the sequences (@pxref{Sequences}) and tree (@pxref{Tree})). Specific options are: @table @command @item optimization.topology = @{boolean@} Tell if topology has to be estimated. @item output.tree.file = @{@{path@}|none@} Where to print the output file. @item bootstrap.number = @{int>0@} Number of bootstrap replicates to perform. @item bootstrap.output.file = @{@{path@}|none@} Where to write bootstrap trees. @end table @c ------------------------------------------------------------------------------------------------------------------ @node bppconsense, bppreroot, bpppars, Reference @section BppConsense: Bio++ Consensus Trees Probably one of the simplest program to use in the suite, just takes a list of trees (for instance produced by BppML, BppDist or BppPars with the bootstrap option enabled) and compute bootstrap values for a reference tree, provided as input, or constructed using a consensus method. The program uses the multiple-trees reading options for input (@pxref{Tree}) and single-tree writing options for output. There are only specific options here: @table @command @item tree = @{tree methods@} The method to use for getting the reference tree. Available function are: @table @command @item Input The tree is loaded using the single-tree reading options (@pxref{Tree}). @item Consensus(threshold = @{int[0,1]@}) Build a consensus tree according to a given threshold. 0 will output a fully resolved tree, 0.5 corresponds to the majority rule and 1 to the strict consensus, but any intermediate value can be specified. @end table @end table @c ------------------------------------------------------------------------------------------------------------------ @node bppreroot, bppseqman, bppconsense, Reference @section BppReroot: Bio++ Serial Tree Re-rooting @table @command @item input.trees.file=@{path@} A path toward multi-trees file (newick). @item outgroups.file=@{path@} A path toward a file containing the different levels of outgroups. @item print.option=@{boolean@} If set to true, the unrootable trees are printed as unrooted in the output file, otherwise the unrootable trees are not printed. @item tryAgain.option=@{boolean@} If set to true and ReRoot finds a non-monophyletic outgroup, it tries the next outgroup. Otherwise, if ReRoot finds a non-monophyletic outgroup, the analysis for this tree is interrupted. No more outgroup are analysed. @item output.trees.file=@{path@} File where to write the rerooted trees. @end table @c ------------------------------------------------------------------------------------------------------------------ @node bppseqman, bppalnscore, bppreroot, Reference @section BppSeqMan: Bio++ Sequence Manipulation The Bio++ Sequence Manipulator convert between various file formats, and can also perform various operations on sequences. It uses the common options for setting the alphabet, loading the sequences (@pxref{Sequences}) and writing the resulting data set (@pxref{WritingSequences}). It can use the ``Generic'' option for alphabets if only file format conversion is to be performed, but the correct alphabet must be specified for more advanced manipulations, like in silico molecular biology. BppSeqMan can perform any number of elementary operation, in any order, providing the output of operation n is compatible with input of operation n+1, and that the input of operation 1 is compatible with the input data. Specific options: @table @command @item input.alignment = @{boolean@} Are the input sequence aligned? If so site selection and filtering is enabled and can be used to preprocess the input data. @item sequence.manip = @{list@} The list, in appropriate order, of elementary operations to perform. See below for a list of these operations. @end table @table @option @item Complement [[alphabet = DNA or RNA]] Convert to the complementary sequence, keeping the original alphabet. @item Transcript [[alphabet = DNA or RNA]] Convert to the complementary sequence, switching the type of alphabet (DNA<->RNA). @item Switch [[alphabet = DNA or RNA]] Change the alphabet type (DNA<->RNA). @item Translate [[alphabet = DNA or RNA]] Convert to proteins. The genetic code used for translation is set via the genetic_code option. Genetic code is set once for all sequences. @item Invert Invert the sequence 5' <-> 3' or N <-> C @item RemoveGaps Remove all gaps in sequences (ie, 'unalign'). @item GapToUnknown Change gaps to fully unresolved characters, N for nucleotides and X for proteins. @item UnknownToGap Change (partially) unresolved characters to gaps. @item RemoveStops Remove all stop codons in sequences. If sequences are aligned, stop codons will be replaced by gaps. The genetic code used for translation is set via the genetic_code option. Genetic code is set once for all sequences. @item RemoveEmptySequences Remove all empty sequences (ie sequences with only gaps). @item RemoveColumnsWithStop Remove all sites with at least one stop codon. The genetic code used for translation is set via the genetic_code option. Genetic code is set once for all sequences. @item GetCDS Remove the first stop codon and everything after in codon sequences. @item CoerceToAlignment Try to convert a set of sequence to an alignment. This will fail if sequences do not have the same length. This step is required before trying commands 'ResolveDotted' or 'KeepComplete'. @item ResolveDotted(alphabet=@{RNA|DNA|Proteins@}) [[Aligned sequences]] Convert a human-readable alignment to a machine-readable alignment. This manipulation must be first if it is used, and the data must be load with the @option{Generic} alphabet. @option{alphabet}: The alphabet to use in order to resolve a dotted alignment. @item KeepComplete(maxGapAllowed=@{int>0@} or @{float[0,100]@}+%) [[Aligned sequences]] Keep only complete sites, ie sites without any gap. Sites with unresolved characters are not removed. It is also possible to fix a maximum proportion of gaps, see specific options. @option{maxGapAllowed}: The maximum proportion of gaps allowed. @item GetCodonPosition(position=@{1|2|3@}) Retrieve the given positions from codon sequences (aligned or not). @item FilterFromTree(tree.file=@{path@}, tree.format=@{chars@}) Get a subset of sequences based on a tree file. The order of sequences in the file will reflect the tree structure. All sequences which do not have a corresponding leaf in the tree, based on the sequence name, will be removed. This method can therefore be used for subsetting a list of sequences, and/or rearrange them in a more convenient manner. @end table Examples of use: @itemize @bullet @item Just change file format: @cartouche @example sequence.manip= @end example @end cartouche @item Change DNA to RNA: @cartouche @example sequence.manip=Switch @end example @end cartouche @item Unalign sequences, perform transcription and translate to proteins: @cartouche @example sequence.manip=RemoveGaps,Transcript,Translate @end example @end cartouche @item Change all unresolved characters to gaps and keep only positions with less than 5 gaps: @cartouche @example sequence.manip=UnknownToGap,KeepComplete(maxGapAllowed=5) @end example @end cartouche @item Keep only positions with less than 30% of gaps, and change them to unresolved characters: @cartouche @example sequence.manip=KeepComplete(maxGapAllowed=30%),GapToUnknown @end example @end cartouche @end itemize @c ------------------------------------------------------------------------------------------------------------------ @node bppalnscore, bpppopstats, bppseqman, Reference @section BppAlnScore: Bio++ Alignment Scoring This program compares two alignments and computes column scores. Scores are output to a text file, and/or can be used to generate a site selection, to be output in a mase file. The two input alignments are specified using the input.sequences procedures (@pxref{Sequences}), with suffixes ``.test'' for the first one, and ``.ref'' for the second. Scores will be computed for each column of the ``.test'' alignment. Two scores are computed, following work by Thompson (1999): @table @emph @item column score (CS) is 1 if the column is found in the reference alignment, 0 otherwise. @item sum-of-pairs score (SPS) is the proportion of pairs of residues which are also aligned in the reference alignment. @end table Specific options: @table @command @item output.scores = @{path@} A text file where scores can be written, one row per column. If set to 'none', no file will be produced. @item output.mase = @{path@} If not 'none', a Mase alignment will be generated, as a copy of the ``.test'' input alignment, with two sites selections names CS and SPS. @item output.sps_thresholds = @{float@} The threshold to use for generating the site selection based on SPS score. All positions with at least the threshold value will be included in the selection. @item score.word_size = @{int>0@} If alignment is for a word alphabet (typically codons), the word size can be specified in order to produce a compatible site selection. Please note that in this case, the alignment must not be loaded with the world alphabet, but the corresponding letter alphabet. @item score.phase = @{int>0|chars@} Eather a number (1-based) stating the starting position for words, or the starting word. In this latter case, the first occurrence of the word in all sequences will be used to determine the phase. @end table @c ------------------------------------------------------------------------------------------------------------------ @node bpppopstats, bpptreedraw, bppalnscore, Reference @section BppPopStats: Bio++ Population Genetics Statistics The @command{BppPopStats} program computes population genetics statistics from a sequence input alignement. It can compute glabal alignment statistics, as well as site-specific statistics. In the first case, results are output on screen or in a log file. In the second case, results are written in a table file, with one site per line. Statistics available also depend on the type on input data (coding or non-coding). @command{BppPopStats} recognizes the standard options for alphabet and genetic code, in case a codon alphabet was specified. Sequences will be considered as coding if encoded with a codon alphabet, and non-coding otherwise. @subsection Specific options @table @command @item input.sequence.file.ingroup = @{path@} Path toward the file containing the ingroup sequences. @item input.sequence.format.ingroup = @{string@} Alignment input format, following standard options. @item input.sequence.file.outgroup = @{path@} Path toward the file containing the outgroup sequences. @item input.sequence.format.outgroup = @{string@} Alignment input format, following standard options. @item input.sequence.file = @{path@} Path toward the file containing all sequences. This option is only recognized if @command{input.sequence.file.ingroup} was not specified. @item input.sequence.format = @{string@} Alignment input format, following standard options. @item input.sequence.outgroup.index = @{[int>0]@} Vector of positions indicating the positions of the outgroup sequences in the alignment. This option is only recognized if @command{input.sequence.file.ingroup} was not specified. @item input.sequence.outgroup.name = @{[string]@} Vector of sequence names indicating the positions of the outgroup sequences in the alignment. This option is only recognized if @command{input.sequence.file.ingroup} was not specified. @item input.sequence.stop_codons_policy = Keep|RemoveIfLast|RemoveAll Tells what to do with positions containing at least one stop codon: keep them, remove them only if they are at the end of the alignment, or remove them all. @item estimate.kappa = @{[boolean]@} Tells if the ratio of transitions / transversion should be estimated from the data and used for further analyses. If yes, kappa will be estimated by maximum likelihood using a model of (codon) sequence evolution. @item estimate.ancestor = @{[boolean]@} If an outgroup sequence is present, it will be used to estimate the ancestral allele for each polymorphic position. A model of (codon) sequence evolution will be used with a marginal ancestral state reconstruction method. @item estimate.sample_ingroup = @{[bollean]@} Tell if a random subset of ingroup sequences should be used to fit model (speeds up calculations in case of large data sets). @item estimate.sample_ingroup.size = @{[integer]@} Number of ingroup sequences to sample. @item pop.stats = @{[string]@} The list of statistics to compute. The next section describes all available statistics. @item logfile = @{path@} Optional file where to output results. @end table @subsection Available statistics @table @command @item SiteFrequencies Output the number of segregating sites as well as the number of singletons. @item Watterson75 Compute Watterson's nucleotide diversity estimator (theta, averaged per site). @item Tajima83 Compute Tajima's nucleotide diversity estimator (pi, averaged per site). @item TajimaD Compute Tajima's D. If a codon alignment is specified (and alphabet is set to codon type), the @command{positions} argument further allow to compute Tajima's D on synonymous sites only (@command{positions=synonymous}), non-synonymous sites (@command{positions=non-synonymous}). Default is to use all sites (@command{positions=all}). @item FuAndLiDStar | FuAndLiFStar Compute Fu and Li's (1993) D and F statistics. If argument @command{tot_mut} is set to yes, then the total number of mutations is used in the calculation, instead of the number of segregating sites (default). @item PiN_PiS For codon sequences only, obviously. Compute nucleotide diversity at synonymous and non-synonymous site, the number of synonymous and non-synonymous sites, as well as the weighted ratio (PiN / NbN) / (PiS / NbS). @item dN_dS For codon sequences only. Build the consensus sequence of both ingroup and outgroup alignments and fit a Yang and Nielsen model of codon sequence evolution with a maximum likelihood approach. Reports the estimated parameters omega (dN / dS ratio) and kappa (transitions / transversions ratio), as well as the divergence between the two sequences. @item MKT Compute the MacDonald-Kreitman table, for codon sequences with outgroup. @item CodonSitesStatistics Generate a table with codon-site specifics statistics, including: @itemize @bullet @item Whether the site is complete or not @item Number of distinct states @item Minor allele frequency @item Major allele frequency @item Minor allele @item Major allele @item State in the first outgroup sequence, if any @item Ancestral state, if computed @item Mean number of synonymous positions for polymorphism @item Whether the site is synonymous polymorphic @item Whether the site is four-fold degenerated @item Non-synonymous diversity (piN) @item Synonymous diversity (piS) @item Mean number of synonymous positions for divergence @item dN, if an outgroup is available @item dS, if an outgroup is available @end itemize The @command{output.file} argument allows to specify the output file (mandatory). @end table @c ------------------------------------------------------------------------------------------------------------------ @node bpptreedraw, , bpppopstats, Reference @section BppTreeDraw: Bio++ Tree Drawing This is a simple program that outputs a tree in various vector formats. It takes as input a tree following the standard syntax. Specific options: @table @command @item output.drawing.file = @{path@} The file where to output the figure. @item output.drawing.format = @{Svg|Xfig|Inkscape|Pgf@} The file format. @item output.drawing.plot = @{plotting algorithm@} The plotting algorithm can be either Phylogram or Cladogram. They follow the keyval syntax, with the following arguments: @end table @table @option @item xu, yu @{float@} The scale units for x and y axis. @item direction.h @{left2right|right2left@} Horizontal orientation of the tree plot. @item direction.v @{top2bottom|bottom2top@} Vertical orientation of the tree plot. @item draw.leaves, draw.ids, draw.brlen, draw.bs @{boolean@} Tell if leaf names, node ids, branch lengths and/or bootstrap should be drawn. @end table @c ------------------------------------------------------------------------------------------------------------------ @c ------------------------------------------------------------------------------------------------------------------ @c end of document @c @node Index, , Reference, Top @c @unnumbered Index @c @c @printindex cp @bye bppsuite-2.4.1/man/000077500000000000000000000000001333524216000141235ustar00rootroot00000000000000bppsuite-2.4.1/man/CMakeLists.txt000066400000000000000000000027471333524216000166750ustar00rootroot00000000000000# CMake script for Bio++ Program Suite # Authors: # Julien Dutheil # Francois gindraud (2017) # Created: 22/08/2009 # Build manpages. # In practice, they are just compressed from the text files using COMPRESS_PROGRAM # Manpages are built and installed as part of "all" if a COMPRESS_PROGRAM is found. # Take all manpages files in the directory file (GLOB manpage_files RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} *.1) if (NOT COMPRESS_BIN) # Just install manpages from source foreach (manpage_file ${manpage_files}) install (FILES ${CMAKE_CURRENT_SOURCE_DIR}/${manpage_file} DESTINATION ${CMAKE_INSTALL_MANDIR}/man1) endforeach (manpage_file) else () # Create a list of manpage targets set (manpage-targets) foreach (manpage_file ${manpage_files}) # Compress manpage, install, add to manpage target list set (input ${CMAKE_CURRENT_SOURCE_DIR}/${manpage_file}) set (output ${CMAKE_CURRENT_BINARY_DIR}/${manpage_file}.${COMPRESS_EXT}) add_custom_command ( OUTPUT ${output} COMMAND ${COMPRESS_BIN} ${COMPRESS_ARGS} ${input} > ${output} DEPENDS ${input} COMMENT "Compressing manpage ${manpage_file}" VERBATIM ) install (FILES ${output} DESTINATION ${CMAKE_INSTALL_MANDIR}/man1) list (APPEND manpage-targets ${output}) unset (input) unset (output) endforeach (manpage_file) # Add target "man", built with "all" (needed because install will fail if not built). add_custom_target (man ALL DEPENDS ${manpage-targets}) endif () bppsuite-2.4.1/man/bppalnscore.1000066400000000000000000000011741333524216000165200ustar00rootroot00000000000000.TH BPPALNSCORE 1 LOCAL .SH NAME bppalnscore - Bio++ alignment scoring .SH SYNOPSIS .B bppalnscore [options] .SH AVAILABILITY All UNIX flavors .SH DESCRIPTION bppalnscore compares two alignment and compute corresponding column scores. Scores can be output to a text file, and/or used to generate a site selection to be output as a Mase file. .SH OPTIONS You should refer to 'info bppsuite' or to the online manual of bppsuite for a complete list of available options. .TP 5 --noninteractive generates output for redirection in a file. .TP param=file reads a file for loading options .SH AUTHOR Bio++ Development Team. bppsuite-2.4.1/man/bppancestor.1000066400000000000000000000011211333524216000165200ustar00rootroot00000000000000.TH BPPANCESTOR 1 LOCAL .SH NAME bppml - Ancestral sequence reconstruction with Bio++ .SH SYNOPSIS .B bppancestor [options] .SH AVAILABILITY All UNIX flavors .SH DESCRIPTION bppancestor performs ancestral sequence reconstructions under a large variety of models, including non-homogeneous ones. .SH OPTIONS You should refer to 'info bppsuite' or to the online manual of bppsuite for a complete list of available options. .TP 5 --noninteractive generates output for redirection in a file. .TP param=file reads a file for loading options .SH AUTHOR The Bio++ Development Team. bppsuite-2.4.1/man/bppconsense.1000066400000000000000000000010451333524216000165240ustar00rootroot00000000000000.TH BPPCONSENSE 1 LOCAL .SH NAME bppconsense - Tree consensus analysis with Bio++ .SH SYNOPSIS .B bppconsense [options] .SH AVAILABILITY All UNIX flavors .SH DESCRIPTION bppconsense performs tree consensus construction under a large variety of rules. .SH OPTIONS You should refer to 'info bppsuite' or to the online manual of bppsuite for a complete list of available options. .TP 5 --noninteractive generates output for redirection in a file. .TP param=file reads a file for loading options .SH AUTHOR The Bio++ Development Team. bppsuite-2.4.1/man/bppdist.1000066400000000000000000000011071333524216000156510ustar00rootroot00000000000000.TH BPPDIST 1 LOCAL .SH NAME bppdist - Distance methods for phylogenetic reconstruction with Bio++ .SH SYNOPSIS .B bppdist [options] .SH AVAILABILITY All UNIX flavors .SH DESCRIPTION bppdist performs phylogenetic reconstruction using distance methods (like neighbor joining or bioNJ). .SH OPTIONS You should refer to 'info bppsuite' or to the online manual of bppsuite for a complete list of available options. .TP 5 --noninteractive generates output for redirection in a file. .TP param=file reads a file for loading options .SH AUTHOR The Bio++ Development Team. bppsuite-2.4.1/man/bppmixedlikelihoods.1000066400000000000000000000015311333524216000202440ustar00rootroot00000000000000.TH BPPANCESTOR 1 LOCAL .SH NAME bppmixedlikelihoods - Computation of site per site likelihoods of components of mixture models. .SH SYNOPSIS .B bppmixedlikelihood [options] .SH AVAILABILITY All UNIX flavors .SH DESCRIPTION On the basis of a mixed model, bppmixedlikelihood computes the likelihood of each site for each submodel of the mixture. This is done with homogeneous and non-homogeneous modelings. If the mixture is based on several values of a parameter, the site per site a posteriori probabilities and average value of this parameter are computed. .SH OPTIONS You should refer to 'info bppsuite' or to the online manual of bppsuite for a complete list of available options. .TP 5 --noninteractive generates output for redirection in a file. .TP param=file reads a file for loading options .SH AUTHOR The Bio++ Development Team. bppsuite-2.4.1/man/bppml.1000066400000000000000000000010401333524216000153120ustar00rootroot00000000000000.TH BPPML 1 LOCAL .SH NAME bppml - Maximum likelihood phylogenetic analysis with Bio++ .SH SYNOPSIS .B bppml [options] .SH AVAILABILITY All UNIX flavors .SH DESCRIPTION bppml performs maximum likelihood (ML) estimation of phylogenies and models. .SH OPTIONS You should refer to 'info bppsuite' or to the online manual of bppsuite for a complete list of available options. .TP 5 --noninteractive generates output for redirection in a file. .TP param=file reads a file for loading options .SH AUTHOR The Bio++ Development Team. bppsuite-2.4.1/man/bpppars.1000066400000000000000000000010251333524216000156520ustar00rootroot00000000000000.TH BPPPARS 1 LOCAL .SH NAME bpppars - Parsimony phylogenetic analysis with Bio++ .SH SYNOPSIS .B bpppars [options] .SH AVAILABILITY All UNIX flavors .SH DESCRIPTION bpppars performs parsimony reconstruction of phylogenies and models. .SH OPTIONS You should refer to 'info bppsuite' or to the online manual of bppsuite for a complete list of available options. .TP 5 --noninteractive generates output for redirection in a file. .TP param=file reads a file for loading options .SH AUTHOR The Bio++ Development Team. bppsuite-2.4.1/man/bpppopstats.1000066400000000000000000000010751333524216000165670ustar00rootroot00000000000000.TH BPPSEQMAN 1 LOCAL .SH NAME bpppopstats - Population genetics with Bio++ .SH SYNOPSIS .B bpppopstats [options] .SH AVAILABILITY All UNIX flavors .SH DESCRIPTION bpppopstats computes several population genetics statistics such as nucleotide diversity, tests for selection etc. .SH OPTIONS You should refer to 'info bppsuite' or to the online manual of bppsuite for a complete list of available options. .TP 5 --noninteractive generates output for redirection in a file. .TP param=file reads a file for loading options .SH AUTHOR Bio++ Development Team. bppsuite-2.4.1/man/bppreroot.1000066400000000000000000000010361333524216000162210ustar00rootroot00000000000000.TH BPPREROOT 1 LOCAL .SH NAME bppreroot - Sequential rerooting of trees with Bio++ .SH SYNOPSIS .B bppreroot [options] .SH AVAILABILITY All UNIX flavors .SH DESCRIPTION bppreroot reroots a set of trees according to a list of outgroup species. .SH OPTIONS You should refer to 'info bppsuite' or to the online manual of bppsuite for a complete list of available options. .TP 5 --noninteractive generates output for redirection in a file. .TP param=file reads a file for loading options .SH AUTHOR The Bio++ Development Team. bppsuite-2.4.1/man/bppseqgen.1000066400000000000000000000011051333524216000161660ustar00rootroot00000000000000.TH BPPSEQGEN 1 LOCAL .SH NAME bppseqgen - Sequence simulation with Bio++ .SH SYNOPSIS .B bppseqgen [options] .SH AVAILABILITY All UNIX flavors .SH DESCRIPTION bppml performs sequence simulation under a given phylogeny or ancestral recombination graph and a large variety of models. .SH OPTIONS You should refer to 'info bppsuite' or to the online manual of bppsuite for a complete list of available options. .TP 5 --noninteractive generates output for redirection in a file. .TP param=file reads a file for loading options .SH AUTHOR The Bio++ Development Team. bppsuite-2.4.1/man/bppseqman.1000066400000000000000000000013521333524216000161740ustar00rootroot00000000000000.TH BPPSEQMAN 1 LOCAL .SH NAME bppseqman - Bio++ sequence manipulation and in silico molecular biology with Bio++ .SH SYNOPSIS .B bppseqman [options] .SH AVAILABILITY All UNIX flavors .SH DESCRIPTION bppseqman performs several in silico molecular biology operations like transcription, translation or traduction. It also allows conversion between various file formats, and bioinformatics tasks like removing of gaps, unknown characters or stop codons. .SH OPTIONS You should refer to 'info bppsuite' or to the online manual of bppsuite for a complete list of available options. .TP 5 --noninteractive generates output for redirection in a file. .TP param=file reads a file for loading options .SH AUTHOR Bio++ Development Team. bppsuite-2.4.1/man/bpptreedraw.1000066400000000000000000000012051333524216000165220ustar00rootroot00000000000000.TH BPPTREEDRAW 1 LOCAL .SH NAME bpptreedraw - Phylogenetic tree drawing with Bio++ .SH SYNOPSIS .B bpptreedraw [options] .SH AVAILABILITY All UNIX flavors .SH DESCRIPTION bpptreedraw generates a figure of a phylogenetic tree in vector format (SVG, LaTex/PGF, Fig), so that it can be easily edited with a dedicated software like Inkscape or XFig. .SH OPTIONS You should refer to 'info bppsuite' or to the online manual of bppsuite for a complete list of available options. .TP 5 --noninteractive generates output for redirection in a file. .TP param=file reads a file for loading options .SH AUTHOR The Bio++ Development Team.