debian/0000755000000000000000000000000012177655625007206 5ustar debian/control0000644000000000000000000000372212176160455010604 0ustar Source: phyml Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Section: science Priority: optional Build-Depends: debhelper (>= 9), autotools-dev, dh-autoreconf Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/phyml/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/phyml/trunk/ Homepage: http://www.atgc-montpellier.fr/phyml Package: phyml Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: Phylogenetic estimation using Maximum Likelihood PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. It provides a wide range of options that were designed to facilitate standard phylogenetic analyses. The main strengths of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. It also implements two methods to evaluate branch supports in a sound statistical framework (the non-parametric bootstrap and the approximate likelihood ratio test). . PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can be analyzed. In practice however, the amount of memory required to process a data set is proportional of the product of the number of sequences by their length. Hence, a large number of sequences can only be processed provided that they are short. Also, PhyML can handle long sequences provided that they are not numerous. With most standard personal computers, the “comfort zone” for PhyML generally lies around 3 to 500 sequences less than 2,000 character long. . This pakcage also includes PhyTime. debian/phyml.doc-base0000644000000000000000000000031211667613727011732 0ustar Document: phyml Title: PhyML — Manual Author: Stéphane Guindon Abstract: Describes how to install and use PhyML. Section: Science/Biology Format: PDF Files: /usr/share/doc/phyml/phyml_manual.pdf debian/rules0000755000000000000000000000204212176161645010255 0ustar #!/usr/bin/make -f # debian/rules for phyml %: dh $@ --with autoreconf override_dh_autoreconf: dh_autoreconf --as-needed override_dh_auto_configure: override_dh_auto_build: # According to README you need different configure options to get different executables # Here we hack in a full build process for phyml executable dh_auto_configure dh_auto_build -- LDFLAGS="$(LDFLAGS)" # move phyml binary to temporary dir inside debian/ $(MAKE) prefix=$(CURDIR)/debian install $(MAKE) distclean dh_auto_configure -- --enable-phytime dh_auto_build -- LDFLAGS="$(LDFLAGS)" override_dh_auto_install: dh_auto_install # install phyml binary we have kept safe above mv $(CURDIR)/debian/bin/* $(CURDIR)/debian/phyml/usr/bin override_dh_auto_clean: dh_auto_clean # remove temporary bin dir for phyml (see above hack) rm -rf debian/bin override_dh_installdocs: dh_installdocs mv $(CURDIR)/debian/phyml/usr/share/doc/phyml/phyml-manual.pdf $(CURDIR)/debian/phyml/usr/share/doc/phyml/phyml_manual.pdf override_dh_compress: dh_compress --exclude=.pdf debian/manpages0000644000000000000000000000001311526252444010703 0ustar debian/*.1 debian/watch0000644000000000000000000000037012170713003010211 0ustar version=3 opts=downloadurlmangle=s|^(http:)//code\.google\.com(//phyml\.googlecode\.com/)|$1$2| \ http://code.google.com/p/phyml/downloads/list?can=3&q=PhyML+Sources \ .*/phyml(?:-|\.|_|_v)(\d\S*)\.(?:tar\.xz|txz|tar\.bz2|tbz2|tar\.gz|tgz|zip|jar) debian/upstream0000644000000000000000000000244112176173754010767 0ustar Archive: Google code Contact: Stephane Guindon Name: PhyML Homepage: http://www.atgc-montpellier.fr/phyml Reference: - author: Stéphane Guindon title: Bayesian estimation of divergence times from large sequence alignments journal: Molecular Biology and Evolution year: 2010 volume: 27 number: 8 pages: 1768-81 doi: 10.1093/molbev/msq060 PMID: 20194424 URL: http://mbe.oxfordjournals.org/content/early/2010/03/01/molbev.msq060.abstract eprint: http://mbe.oxfordjournals.org/content/early/2010/03/01/molbev.msq060.full.pdf+html - author: Guindon, Stephane and Gascuel, Olivier title: A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood journal: Syst Biol volume: 52 number: 5 pages: 696-704 doi: 10.1080/10635150390235520 year: 2003 URL: http://sysbio.oxfordjournals.org/cgi/content/abstract/52/5/696 eprint: http://sysbio.oxfordjournals.org/cgi/reprint/52/5/696.pdf PMID: 14530136 Repository: http://phyml.googlecode.com/svn/trunk/ Repository-Browse: http://code.google.com/p/phyml/source/browse/ Watch: | version=3 http://code.google.com/p/phyml/downloads/list \ http://phyml[.]googlecode[.]com/files/phyml_(20.*)[.]tar[.]gz Webservice: http://www.atgc-montpellier.fr/phyml debian/copyright0000644000000000000000000002075112176127275011140 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: http://phyml.googlecode.com/files/phyml-20120412.tar.gz Files: * Copyright: Stephane Guindon Olivier Gascuel Jean-Francois Dufayard Wim Hodrijk Franck Lethiec License: GPL-2+ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. Comment: On the Debian operating system, a copy of the GNU GPL version 2 can be found in ‘/usr/share/common-licenses/GPL-2’. Files: doc/phyml_manual.ps Copyright: © 1999 - 2008 by PhyML Development Team © 1996 Craig Barratt, Michael C. Grant, and David Carlisle. © 1997, 2009 American Mathematical Society () License: mixture In my understanding, the text (GPL-2+) is only aggregated with the font (OFL-1.1) and the PostScript code (psfrag). CP, 2011-06-26. Files: src/depcomp Copyright: © 1999, 2000, 2003, 2004, 2005 Free Software Foundation, Inc. License: GPL-2+ with Autoconf exception This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. . As a special exception to the GNU General Public License, if you distribute this file as part of a program that contains a configuration script generated by Autoconf, you may include it under the same distribution terms that you use for the rest of that program. Files: /src/missing Copyright: © 1996, 1997 Free Software Foundation, Inc. © Franc,ois Pinard , 1996. License: GPL-2+ (see above) Files: src/install-sh Copyright: © 1991 by the Massachusetts Institute of Technology License: install-sh Permission to use, copy, modify, distribute, and sell this software and its documentation for any purpose is hereby granted without fee, provided that the above copyright notice appear in all copies and that both that copyright notice and this permission notice appear in supporting documentation, and that the name of M.I.T. not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission. M.I.T. makes no representations about the suitability of this software for any purpose. It is provided "as is" without express or implied warranty. Files: debian/* Copyright: © 2009 Charles Plessy License: same-as-phyml See above. License: OFL-1.1 SIL OPEN FONT LICENSE . Version 1.1 - 26 February 2007 . PREAMBLE . The goals of the Open Font License (OFL) are to stimulate worldwide development of collaborative font projects, to support the font creation efforts of academic and linguistic communities, and to provide a free and open framework in which fonts may be shared and improved in partnership with others. . The OFL allows the licensed fonts to be used, studied, modified and redistributed freely as long as they are not sold by themselves. The fonts, including any derivative works, can be bundled, embedded, redistributed and/or sold with any software provided that any reserved names are not used by derivative works. The fonts and derivatives, however, cannot be released under any other type of license. The requirement for fonts to remain under this license does not apply to any document created using the fonts or their derivatives. . DEFINITIONS . "Font Software" refers to the set of files released by the Copyright Holder(s) under this license and clearly marked as such. This may include source files, build scripts and documentation. . "Reserved Font Name" refers to any names specified as such after the copyright statement(s). . "Original Version" refers to the collection of Font Software components as distributed by the Copyright Holder(s). . "Modified Version" refers to any derivative made by adding to, deleting, or substituting — in part or in whole — any of the components of the Original Version, by changing formats or by porting the Font Software to a new environment. . "Author" refers to any designer, engineer, programmer, technical writer or other person who contributed to the Font Software. . PERMISSION & CONDITIONS . Permission is hereby granted, free of charge, to any person obtaining a copy of the Font Software, to use, study, copy, merge, embed, modify, redistribute, and sell modified and unmodified copies of the Font Software, subject to the following conditions: . 1) Neither the Font Software nor any of its individual components, in Original or Modified Versions, may be sold by itself. . 2) Original or Modified Versions of the Font Software may be bundled, redistributed and/or sold with any software, provided that each copy contains the above copyright notice and this license. These can be included either as stand-alone text files, human-readable headers or in the appropriate machine-readable metadata fields within text or binary files as long as those fields can be easily viewed by the user. . 3) No Modified Version of the Font Software may use the Reserved Font Name(s) unless explicit written permission is granted by the corresponding Copyright Holder. This restriction only applies to the primary font name as presented to the users. . 4) The name(s) of the Copyright Holder(s) or the Author(s) of the Font Software shall not be used to promote, endorse or advertise any Modified Version, except to acknowledge the contribution(s) of the Copyright Holder(s) and the Author(s) or with their explicit written permission. . 5) The Font Software, modified or unmodified, in part or in whole, must be distributed entirely under this license, and must not be distributed under any other license. The requirement for fonts to remain under this license does not apply to any document created using the Font Software. . TERMINATION . This license becomes null and void if any of the above conditions are not met. . DISCLAIMER . THE FONT SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO ANY WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT OF COPYRIGHT, PATENT, TRADEMARK, OR OTHER RIGHT. IN NO EVENT SHALL THE COPYRIGHT HOLDER BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, INCLUDING ANY GENERAL, SPECIAL, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF THE USE OR INABILITY TO USE THE FONT SOFTWARE OR FROM OTHER DEALINGS IN THE FONT SOFTWARE. License: psfrag All rights are reserved. . This system is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. Don't come complaining to us if you modify this file and it doesn't work! If this file is modified by anyone but the authors, those changes and their authors must be explicitly stated HERE. Comment: see the following URLs: ftp://ftp.riken.jp/pub/tex-archive/macros/latex/contrib/psfrag/psfrag.dtx http://www.ctan.org/tex-archive/macros/latex/contrib/psfrag . Psfrag seems to have been accepted in main, so I suppose that the absence of explicit authorisation of redistributing the work has been clarified… . texlive-latex-recommended: /usr/share/texmf-texlive/tex/latex/psfrag/psfrag.sty debian/source/0000755000000000000000000000000012176127404010472 5ustar debian/source/format0000644000000000000000000000001411473514012011672 0ustar 3.0 (quilt) debian/README.Debian0000644000000000000000000000045312176176411011237 0ustar phyml for Debian ---------------- In principle it is possible to create a package of the parallelised version phyml-mpi from the same source. Please contact the maintainer of this package in case you need this for your work. -- Andreas Tille Wed, 31 Jul 2013 13:55:11 +0200 debian/changelog0000644000000000000000000000744212177655554011070 0ustar phyml (2:20120412-2) unstable; urgency=low * debian/patches/sse_only_if_supported.patch: Check architecture before deciding to build using -msse Closes: #718747 -- Andreas Tille Mon, 05 Aug 2013 09:56:27 +0200 phyml (2:20120412-1) unstable; urgency=low [ Charles Plessy ] * New upstream version. * Updated watch file to track stable versions only. * debian/rules, debian/docs, the manual is now phyml-manual.pdf. [ Andreas Tille ] * debian/control: - cme fix dpkg-control - debhelper 9 - use anonscm in Vcs fields * debian/rules: - Use dh more consequently to work around two different configure steps - Propagate hardening options * debian/upstream: Additional (newer) publication * debian/phytime.1: Add manpage for phytime based on some html2man output and the abstract of the according publication * debian/README.Debian: Hint to possible phyml-mpi -- Charles Plessy Mon, 15 Jul 2013 09:55:11 +0900 phyml (2:20110919-1) unstable; urgency=low * New upstream version. * Kept manual's old name with no date (debian/docs, debian/rules). * Do not compress PDFs (debian/rules). -- Charles Plessy Mon, 05 Dec 2011 13:19:40 +0900 phyml (2:20110526-1) unstable; urgency=low * New upstream version. * debian/control: - Corrected VCS URLs. - Using debhelper 8 (debian/compat). - Enhances bioperl-run (that has a PhyML wrapper). - Standards-Version incremented to reflect compliance with Policy 3.9.2. * Added build-arch and build-indep targets to debian/rules. * Build and distribute PhyTime (debian/rules, debian/control). -- Charles Plessy Sun, 26 Jun 2011 12:14:54 +0900 phyml (2:20100720-1) unstable; urgency=low * New upstream version * Fixed watch file * Standard-Version: 3.9.1 (no changes needed) * Source format 3.0 (quilt) * Wrote man page -- Andreas Tille Mon, 14 Feb 2011 15:04:52 +0100 phyml (2:20100123-1) unstable; urgency=low * New upstream release. [ Nelson A. de Oliveira ] * Fix watch file. * Increment the epoch number to fix a typo in the version number. [ Charles Plessy ] * Checked conformance with Policy 3.8.4 and incremented Standards-Version in debian/control to reflect this (no changes needed). * Moved the bibliographic reference from debian/reference to debian/upstream-metadata.yaml. * Adapted debian/rules to the new location of the auto(conf|make) files. -- Charles Plessy Sun, 07 Mar 2010 19:55:08 +0900 phyml (1:200900706-2) unstable; urgency=low * Disable parallel building, that was incorrectly supported and induced build failures by race condition (Closes: #536967). -- Charles Plessy Wed, 15 Jul 2009 09:35:40 +0900 phyml (1:200900706-1) unstable; urgency=low * New upstream release. * Suppressed unneeded Lintian overrides, and use ‘dh clean’ in debian/rules. * Checked conformance with Policy 3.8.2 and incremented Standards-Version in debian/control to reflect this (no changes needed). * Experimentation on the format of debian/copyright. -- Charles Plessy Sat, 11 Jul 2009 14:25:23 +0900 phyml (1:20090501-1) unstable; urgency=low * New upstream release clarifying the license of the documentation and switching to a versionning system that can be sorted by numerical order. * Added debian/source.lintian-overrides to indicate that the configure-generated files are deleted at cleaning time. * Using ‘dh binary-arch’ to simplify debian/rules. -- Charles Plessy Sat, 16 May 2009 14:55:14 +0900 phyml (30042009-1) unstable; urgency=low * Initial release (Closes: #517165) -- Charles Plessy Fri, 01 May 2009 08:53:44 +0900 debian/patches/0000755000000000000000000000000012177655455010636 5ustar debian/patches/sse_only_if_supported.patch0000644000000000000000000000252212177655455016276 0ustar Author: Andreas Tille LastChanged: Mon, 05 Aug 2013 09:56:27 +0200 BugsClosed: http://bugs.debian.org/718747 Description: Verify architecture whether we comiple on i386 or amd64 and only in this case use -msse --- a/configure.ac +++ b/configure.ac @@ -48,6 +48,16 @@ AC_CHECK_FUNCS([floor pow rint sqrt strc #;; #esac +case "${host}" in +*i386*|*amd64*|*x86_64*) +MSSE=-msse +AC_MSG_NOTICE("On arch ${host} use MSSE = ${MSSE}") +;; +*) +MSSE= +AC_MSG_NOTICE("Do not use MSSE = ${MSSE} because not available on arch ${host}") +;; +esac dnl CFLAGS="-O3 -fomit-frame-pointer -funroll-loops -Wall ${ARCH_flag}" dnl CFLAGS="-O3 -Wfloat-equal -fomit-frame-pointer -funroll-loops" @@ -65,8 +75,8 @@ AC_ARG_ENABLE([debug], [Remove optimization options and add debug informations.])]) AS_IF([test "x$enable_debug" = "xyes"], [CFLAGS="-ansi -pedantic -Wall -std=c99 -O0 -g"], - dnl [CFLAGS="-ansi -pedantic -Wall -std=c99 -O2 -msse -fomit-frame-pointer -funroll-loops ${ARCH_flag}"]) - [CFLAGS="-Wall -O2 -msse -fomit-frame-pointer -funroll-loops ${ARCH_flag}"]) + dnl [CFLAGS="-ansi -pedantic -Wall -std=c99 -O2 ${MSSE} -fomit-frame-pointer -funroll-loops ${ARCH_flag}"]) + [CFLAGS="-Wall -O2 ${MSSE} -fomit-frame-pointer -funroll-loops ${ARCH_flag}"]) AC_ARG_ENABLE([mpi], debian/patches/series0000644000000000000000000000003412177651452012041 0ustar sse_only_if_supported.patch debian/compat0000644000000000000000000000000212176133064010367 0ustar 9 debian/docs0000644000000000000000000000002512176127275010050 0ustar doc/phyml-manual.pdf debian/phyml.10000644000000000000000000001672511601703560010413 0ustar .TH PhyML "1" "3.0" "phyml " "User Commands" .SH NAME phyml \- Phylogenetic estimation using Maximum Likelihood .SH SYNOPSIS: .PP phyml [command args] .IP All the options below are optional (except '\-i' if you want to use the command\-line interface). .PP Command options: .HP \fB-i\fR (or \fB\-\-input\fR) \fIseq_file_name\fR .IP \fIseq_file_name\fR is the name of the nucleotide or amino\-acid sequence file in PHYLIP format. .PP .HP \fB\-d\fR (or \fB\-\-datatype\fR) \fIdata_type\fR .IP \fIdata_type\fR is 'nt' for nucleotide (default), 'aa' for amino\-acid sequences, or 'generic', (use NEXUS file format and the 'symbols' parameter here). .PP .HP \fB\-q\fR (or \fB\-\-sequential\fR) .IP Changes interleaved format (default) to sequential format. .PP .HP \fB\-n\fR (or \fB\-\-multiple\fR) \fInb_data_sets\fR .IP \fInb_data_sets\fR is an integer corresponding to the number of data sets to analyse. .PP .HP \fB\-p\fR (or \fB\-\-pars\fR) .OP Use a minimum parsimony starting tree. This option is taken into account when the '\-u' option is absent and when tree topoLOGy modifications are to be done. .HP \fB\-b\fR (or \fB\-\-bootstrap\fR) \fIint\fR .IP \fIint > 0:\fR int is the number of bootstrap replicates. .IP \fIint = 0:\fR neither approximate likelihood ratio test nor bootstrap values are computed. .IP \fIint = \-1\fR: approximate likelihood ratio test returning aLRT statistics. .IP \fIint = \-2\fR: approximate likelihood ratio test returning Chi2\-based parametric branch supports. .IP \fIint = \-4\fR: (default) SH\-like branch supports alone. .HP \fB\-m\fR (or \fB\-\-model\fR) \fImodel\fR .IP model : substitution model name. \- \fINucleotide\fR\-based models : \fIHKY85\fR (default) | \fIJC69\fR | \fIK80\fR | \fIF81\fR | \fIF84\fR | \fITN93\fR | \fIGTR\fR | \fIcustom\fR (for the custom option, a string of six digits identifies the model. For instance, 000000) .IP corresponds to F81 (or JC69 provided the distribution of nucleotide frequencies is uniform). 012345 corresponds to GTR. This option can be used for encoding any model that is a nested within GTR. .IP \- \fIAmino\-acid\fR based models : \fILG\fR (default) | \fIWAG\fR | \fIJTT\fR | \fIMtREV\fR | \fIDayhoff\fR | \fIDCMut\fR | \fIRtREV\fR | \fICpREV\fR | \fIVT\fR \fIBlosum62\fR | \fIMtMam\fR | \fIMtArt\fR | \fIHIVw\fR | \fIHIVb\fR | \fIcustom\fR .HP \fB\-\-aa_rate_file\fR \fIfilename\fR .IP \fIfilename\fR is the name of the file that provides the amino acid substitution rate matrix in PAML format. It is compulsory to use this option when analysing amino acid sequences with the `custom' model. .PP .HP \fB\-f\fR \fIe\fR, \fIm\fR, or \fIfA,fC,fG,fT\fR .IP \fIe\fR : the character frequencies are determined as follows : .IP \- Nucleotide sequences: (Empirical) the equilibrium base frequencies are estimated by counting the occurence of the different bases in the alignment. .IP \- Amino\-acid sequences: (Empirical) the equilibrium amino\-acid frequencies are estimated by counting the occurence of the different amino\-acids in the alignment. .IP \fIm\fR : the character frequencies are determined as follows : .IP \- Nucleotide sequences: (ML) the equilibrium base frequencies are estimated using maximum likelihood .IP \- Amino\-acid sequences: (Model) the equilibrium amino\-acid frequencies are estimated using the frequencies defined by the substitution model. .IP \fI"fA,fC,fG,fT"\fR : only valid for nucleotide\-based models. fA, fC, fG and fT are floating numbers that correspond to the frequencies of A, C, G and T respectively (WARNING: do not use any blank space between your values of nucleotide frequencies, only commas!) .HP \fB\-t\fR (or \fB\-\-ts\fR/tv) \fIts/tv_ratio\fR .IP \fIts/tv_ratio\fR : transition/transversion ratio. DNA sequences only. Can be a fixed positive value (ex:4.0) or e to get the maximum likelihood estimate. .HP \fB\-v\fR (or \fB\-\-pinv\fR) \fIprop_invar\fR .IP \fIprop_invar\fR: proportion of invariable sites. Can be a fixed value in the [0,1] range or e to get the maximum likelihood estimate. .HP \fB\-c\fR (or \fB\-\-nclasses\fR) \fInb_subst_cat\fR .IP \fInb_subst_cat\fR : number of relative substitution rate categories. Default: \fInb_subst_cat=4\fR. Must be a positive integer. .HP \fB\-a\fR (or \fB\-\-alpha\fR) \fIgamma\fR .IP \fIgamma\fR : distribution of the gamma distribution shape parameter. Can be a fixed positive value or \fIe\fR to get the maximum likelihood estimate. .HP \fB\-s\fR (or \fB\-\-search\fR) \fImove\fR .IP Tree topoLOGy search operation option. Can be either \fINNI\fR (default, fast) or \fISPR\fR (a bit slower than NNI) or \fIBEST\fR (best of NNI and SPR search). .HP \fB\-u\fR (or \fB\-\-inputtree\fR) \fIuser_tree_file\fR .IP \fIuser_tree_file\fR : starting tree filename. The tree must be in Newick format. .HP \fB\-o\fR \fIparams\fR .IP This option focuses on specific parameter optimisation. .IP \fIparams\fR=tlr : tree topoLOGy (t), branch length (l) and rate parameters (r) are optimised. .IP \fIparams\fR=tl : tree topoLOGy and branch length are optimised. .IP \fIparams\fR=lr : branch length and rate parameters are optimised. .IP \fIparams\fR=l : branch length are optimised. .IP \fIparams\fR=r : rate parameters are optimised. .IP \fIparams\fR=n : no parameter is optimised. .HP \fB\-\-rand_start\fR .IP This option sets the initial tree to random. It is only valid if SPR searches are to be performed. .HP \fB\-\-n_rand_starts\fR \fInum\fR .IP \fInum\fR is the number of initial random trees to be used. It is only valid if SPR searches are to be performed. .HP \fB\-\-r_seed\fR \fInum\fR .IP \fInum\fR is the seed used to initiate the random number generator. Must be an integer. .HP \fB\-\-print_site_lnl\fR .IP Print the likelihood for each site in file *_phyml_lk.txt. .PP .HP \fB\-\-print_trace\fR .IP Print each phyLOGeny explored during the tree search process in file *_phyml_trace.txt. .HP \fB\-\-run_id\fR \fIID_string\fR .IP Append the string \fIID_string\fR at the end of each PhyML output file. This option may be useful when running simulations involving PhyML. .PP .HP \fB\-\-quiet\fR .IP No interactive question (for running in batch mode) and quiet output. .PP .HP \fB\-\-no_memory_check\fR .IP No interactive question for memory usage (for running in batch mode). Normal output otherwise. .PP .HP \fB\-\-alias_subpatt\fR .IP Site aliasing is generalized at the subtree level. Sometimes lead to faster calculations. See Kosakovsky Pond SL, Muse SV, Sytematic Biology (2004) for an example. .PP .HP \fB\-\-boot_progress_display\fR \fInum\fR (default=20) .IP \fInum\fR is the frequency at which the bootstrap progress bar will be updated. Must be an integer. .SH PHYLIP\-LIKE INTERFACE .PP You can also use PhyML with no argument, in this case change the value of a parameter by typing its corresponding character as shown on screen. .SH EXAMPLES .PP DNA interleaved sequence file, default parameters : .IP \fBphyml \-i seqs1\fR .PP AA interleaved sequence file, default parameters : .IP \fBphyml \-i seqs2 \-d aa\fR .TP AA sequential sequence file, with customization : .IP \fBphyml \-i seqs3 \-q \-d aa \-m JTT \-c 4 \-a e\fR .SH "SEE ALSO" .PP A simple, fast, and accurate algorithm to estimate large phyLOGenies by maximum likelihood .PP Stephane Guindon and Olivier Gascuel, Systematic BioLOGy 52(5):696\-704, 2003. .PP Please cite this paper if you use this software in your publications. .SH AUTHOR \fBPhyML\fP was written by Stephane Guindon and Olivier Gascuel and others .PP This manual page was written by Andreas Tille , for the Debian project (but may be used by others). debian/phytime.10000644000000000000000000001243712176175521010745 0ustar .TH PHYTIME "1" "July 2013" "phytime " "User Commands" .SH NAME phytime \- Bayesian estimation of divergence times from large sequence alignments .SH DESCRIPTION Bayesian estimation of divergence times from molecular sequences relies on sophisticated Markov chain Monte Carlo techniques, and Metropolis-Hastings (MH) samplers have been successfully used in that context. This approach involves heavy computational burdens that can hinder the analysis of large phylogenomic data sets. Reliable estimation of divergence times can also be extremely time consuming, if not impossible, for sequence alignments that convey weak or conflicting phylogenetic signals, emphasizing the need for more efficient sampling methods. This article describes a new approach that estimates the posterior density of substitution rates and node times. The prior distribution of rates accounts for their potential autocorrelation along lineages, whereas priors on node ages are modeled with uniform densities. Also, the likelihood function is approximated by a multivariate normal density. The combination of these components leads to convenient mathematical simplifications, allowing the posterior distribution of rates and times to be estimated using a Gibbs sampling algorithm. The analysis of four real-world data sets shows that this sampler outperforms the standard MH approach and demonstrates the suitability of this new method for analyzing large and/or difficult data sets. .SH SYNOPSIS .B phytime [command args] .SH OPTIONS All the options below are optional except '\-i','\-u' and '\-\-calibration'. .PP Command options: .IP \-i (or \fB\-\-input\fR) seq_file_name .IP seq_file_name is the name of the nucleotide or amino\-acid sequence file in PHYLIP format. .PP .HP \fB\-d\fR (or \fB\-\-datatype\fR) data_type .IP data_type is 'nt' for nucleotide (default), 'aa' for amino\-acid sequences, or 'generic', (use NEXUS file format and the 'symbols' parameter here). .PP .HP \fB\-q\fR (or \fB\-\-sequential\fR) .PP Changes interleaved format (default) to sequential format. .PP .HP \fB\-m\fR (or \fB\-\-model\fR) model .IP model : substitution model name. \- Nucleotide\-based models : HKY85 (default) | JC69 | K80 | F81 | F84 | TN93 | GTR | custom (*) (*) : for the custom option, a string of six digits identifies the model. For instance, 000000 .IP corresponds to F81 (or JC69 provided the distribution of nucleotide frequencies is uniform). 012345 corresponds to GTR. This option can be used for encoding any model that is a nested within GTR. .IP \- Amino\-acid based models : LG (default) | WAG | JTT | MtREV | Dayhoff | DCMut | RtREV | CpREV | VT .TP Blosum62 | MtMam | MtArt | HIVw | HIVb | custom .PP .HP \fB\-\-aa_rate_file\fR filename .IP filename is the name of the file that provides the amino acid substitution rate matrix in PAML format. It is compulsory to use this option when analysing amino acid sequences with the `custom' model. .PP .HP \fB\-\-calibration\fR filename .IP filename is the name of the calibration file that provides a priori defined boundaries for node ages. Please read the manual for more information about the format of this file. .PP .HP \fB\-t\fR (or \fB\-\-ts\fR/tv) ts/tv_ratio .IP ts/tv_ratio : transition/transversion ratio. DNA sequences only. Can be a fixed positive value (ex:4.0) or e to get the maximum likelihood estimate. .PP .HP \fB\-v\fR (or \fB\-\-pinv\fR) prop_invar .IP prop_invar : proportion of invariable sites. Can be a fixed value in the [0,1] range or e to get the maximum likelihood estimate. .PP .HP \fB\-c\fR (or \fB\-\-nclasses\fR) nb_subst_cat .IP nb_subst_cat : number of relative substitution rate categories. Default : nb_subst_cat=4. Must be a positive integer. .PP .HP \fB\-a\fR (or \fB\-\-alpha\fR) gamma .IP gamma : distribution of the gamma distribution shape parameter. Can be a fixed positive value or e to get the maximum likelihood estimate. .PP .HP \fB\-u\fR (or \fB\-\-inputtree\fR) user_tree_file .IP user_tree_file : starting tree filename. The tree must be in Newick format. .PP .HP \fB\-\-r_seed\fR num .IP num is the seed used to initiate the random number generator. Must be an integer. .PP .HP \fB\-\-run_id\fR ID_string .IP Append the string ID_string at the end of each PhyML output file. This option may be useful when running simulations involving PhyML. .PP .HP \fB\-\-quiet\fR .IP No interactive question (for running in batch mode) and quiet output. .PP .HP \fB\-\-no_memory_check\fR .IP No interactive question for memory usage (for running in batch mode). Normal output otherwise. .PP .HP \fB\-\-chain_len\fR num .IP num is the number of generations or runs of the Markov Chain Monte Carlo. Set to 1E+6 by default. Must be an integer. .PP .HP \fB\-\-sample_freq\fR num .IP The chain is sampled every num generations. Set to 1E+3 by default. Must be an integer. .PP .HP \fB\-\-no_data\fR .IP Use this option to sample from the priors only (rather from the posterior joint density of the model parameters). .PP .HP \fB\-\-fastlk\fR .IP Use the multivariate normal approximation to the likelihood and speed up calculations .SH SEE ALSO .PP 'Bayesian estimation of divergence times from large sequence alignments.' Stephane Guindon, Molecular Biology and Evolution 27(8):1768\-81, 2010. .PP Please cite this paper if you use this software in your publications.