debian/0000755000000000000000000000000011745344300007167 5ustar debian/watch0000644000000000000000000000013211745236445010226 0ustar version=3 http://ftp.seqan.de/releases/seqan-([.\d]+)\.zip \ debian debian/orig-tar.sh debian/copyright0000644000000000000000000001274711636037220011134 0ustar Format: http://dep.debian.net/deps/dep5/ Source: http://www.seqan.de/uploads/media/Seqan_Release_1.3.zip Files: * Copyright: © 2007-2010 Andreas Döring David Weese Tobias Rausch Stephan Aiche Anne-Katrin Emde Carsten Kemena Konrad Ludwig Moritz Rudolph Marcel H. Schulz. License: LGPL-3+ Files: apps/mason/* apps/rabema/* demos/tutorial/read_mapping/minimapper.cpp Copyright: © 2010 Manuel Holtgrewe, FU Berlin License: GPL-3+ Files: apps/stellar/* Copyright: © 2010 Birte Kehr License: LGPL-3+ Files: cmake/CMake/cuda/FindCUDA/* Copyright: © 2008 - 2009 NVIDIA Corporation. All rights reserved. © 2007-2009 Scientific Computing and Imaging Institute, University of Utah License: MIT-cuda License for the specific language governing rights and limitations under Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: . The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. . THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. Comment: bogus first line ? Files: seqan/* doc/shape_predefined.h Copyright: © 2006-2010, Knut Reinert, FU Berlin License: 3BSD-like Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of Knut Reinert or the FU Berlin nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. . THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Files: seqan/index/index_sa_lss.h Copyright: © 1999, N. Jesper Larsson © 2007 David Weese. License: other This software may be used freely for any purpose. However, when distributed, the original source must be clearly stated, and, when the source code is distributed, the copyright notice must be retained and any alterations in the code must be clearly marked. No warranty is given regarding the quality of this software. License: GPL-3+ 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 3 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, see . Comment: On Debian systems, you can find the GPL license version 3 in ‘/usr/share/common-licenses/GPL-3’. License: LGPL-3+ This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. . This library 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 Lesser General Public License for more details. Comment: On Debian systems, you can find the LGPL license version 3 in ‘/usr/share/common-licenses/LGPL-3’. debian/razers.10000644000000000000000000000704711261043504010562 0ustar .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.36. .TH RAZERS "1" "September 2009" "RazerS version 1.0 20090710 [4739]" "User Commands" .SH NAME RazerS \- Fast Read Mapping with Sensitivity Control .SH SYNOPSIS .B razers [\fIOPTION\fR]... \fI \fR .SH DESCRIPTION RazerS \- Fast Read Mapping with Sensitivity Control .IP razers [OPTION]... .TP \fB\-h\fR, \fB\-\-help\fR displays this help message .TP \fB\-V\fR, \fB\-\-version\fR print version information .SS "Main Options:" .TP \fB\-f\fR, \fB\-\-forward\fR only compute forward matches .TP \fB\-r\fR, \fB\-\-reverse\fR only compute reverse complement matches .TP \fB\-i\fR, \fB\-\-percent\-identity\fR NUM set the percent identity threshold (default 92) .TP \fB\-rr\fR, \fB\-\-recognition\-rate\fR NUM set the percent recognition rate (default 99) .TP \fB\-pd\fR, \fB\-\-param\-dir\fR DIR folder containing user\-computed parameter files (optional) .TP \fB\-id\fR, \fB\-\-indels\fR allow indels (default: mismatches only) .TP \fB\-ll\fR, \fB\-\-library\-length\fR NUM mate\-pair library length (default 220) .TP \fB\-le\fR, \fB\-\-library\-error\fR NUM mate\-pair library length tolerance (default 50) .TP \fB\-m\fR, \fB\-\-max\-hits\fR NUM output only NUM of the best hits (default 100) .TP \fB\-\-unique\fR output only unique best matches (\fB\-m\fR 1 \fB\-dr\fR 0 \fB\-pa\fR) .TP \fB\-tr\fR, \fB\-\-trim\-reads\fR NUM trim reads to given length (default off) .TP \fB\-o\fR, \fB\-\-output\fR FILE change output filename (default .result) .TP \fB\-v\fR, \fB\-\-verbose\fR verbose mode .TP \fB\-vv\fR, \fB\-\-vverbose\fR very verbose mode .SS "Output Format Options:" .TP \fB\-a\fR, \fB\-\-alignment\fR dump the alignment for each match .TP \fB\-pa\fR, \fB\-\-purge\-ambiguous\fR purge reads with more than max\-hits best matches .TP \fB\-dr\fR, \fB\-\-distance\-range\fR NUM only consider matches with at most NUM more errors compared to the best (default output all) .TP \fB\-of\fR, \fB\-\-output\-format\fR NUM set output format (default 0) 0 = Razer format 1 = enhanced Fasta format 2 = Eland format 3 = GFF format .TP \fB\-gn\fR, \fB\-\-genome\-naming\fR NUM select how genomes are named (default 0) 0 = use Fasta id 1 = enumerate beginning with 1 .TP \fB\-rn\fR, \fB\-\-read\-naming\fR NUM select how reads are named (default 0) 0 = use Fasta id 1 = enumerate beginning with 1 2 = use the read sequence (only for short reads!) .TP \fB\-so\fR, \fB\-\-sort\-order\fR NUM select how matches are sorted (default 0) 0 = 1. read number, 2. genome position 1 = 1. genome position, 2. read number .TP \fB\-pf\fR, \fB\-\-position\-format\fR NUM select begin/end position numbering (default 0) 0 = gap space 1 = position space .SS "Filtration Options:" .TP \fB\-s\fR, \fB\-\-shape\fR BITSTRING set k\-mer shape (default 11111111111) .TP \fB\-t\fR, \fB\-\-threshold\fR NUM set minimum k\-mer threshold (default 1) .TP \fB\-oc\fR, \fB\-\-overabundance\-cut\fR NUM set k\-mer overabundance cut ratio (default 1) .TP \fB\-rl\fR, \fB\-\-repeat\-length\fR NUM set simple\-repeat length threshold (default 1000) .TP \fB\-tl\fR, \fB\-\-taboo\-length\fR NUM set taboo length (default 1) .SS "Verification Options:" .TP \fB\-mN\fR, \fB\-\-match\-N\fR \&'N' matches with all other characters .TP \fB\-ed\fR, \fB\-\-error\-distr\fR FILE write error distribution to FILE .SH AUTHOR .br razers was written by David Weese. .PP This manual page was generated using html2man and polished by Soeren Sonnenburg , for the Debian project (but may be used by others). debian/changelog0000644000000000000000000000442711745342422011053 0ustar seqan (1.3.1-1) unstable; urgency=low * New upstream version * debian/watch: Adapt to new way to provide release archives * debian/orig-tar.sh: - Be less noisy - Provide fallback target dir in case .svn/deb-layout doese not exist - which is the case at least in my checkout * debian/control: - Standards-Version: 3.9.3 (no changes needed) - distinct short descriptions * debian/seqan-dev.doc-base: Provide doc-base control file * debian/rules + several debhelper files: Rely more on debhelper than manual moving around files to make debian/rules better maintaineable * debian/rules: - Do not specify single target files but rather use find to obtain files to move around - Save a copy of those files which will be removed by upstream clean target otherwise to enable building twice in a row -- Andreas Tille Mon, 23 Apr 2012 13:25:17 +0200 seqan (1.3-1) unstable; urgency=low * Team upload. * New upstream release (Closes: #640302). [ Charles Plessy ] * Collected various informations in ‘debian/upstream-metadata.yaml’. * Compress the source and binary packages with xz (debian/orig-tar.sh, debian/rules). * Removed convenience code copy of samtools (debian/orig-tar.sh). * Use Debhelper 8 (debian/compat, debian/control). * Conforms to Policy 3.9.2 (debian/control, no other changes needed). * Built using the cmake class of CDBS (debian/rules). * debian/control: - Corrected VCS URLs. - Build-Depend on libboost-dev as Cmake was looking for it. - Build-Depend on zlib1g-dev, as seqan needs to detect zlib to set SEQAN_HAS_SAMTOOLS to 1. - Changed Priority from extra to optional. - Changed sequan-apps Section from libdevel to science. * debian/patch/samtools.patch corrects path to SAMtools headers. * Machine-readable debian/copyright. [ Andreas Tille ] * debian/control - added myself to uploaders - Standards-Version: 3.9.1 (no changes needed) * debian/watch: Also catch RC candidates * debian/source/format: 3.0 (quilt) -- Charles Plessy Fri, 16 Sep 2011 12:51:39 +0900 seqan (1.2-1) unstable; urgency=low * Initial Release (Closes: #487361) -- Soeren Sonnenburg Wed, 30 Sep 2009 20:41:39 +0200 debian/pair_align.10000644000000000000000000000357511261043504011363 0ustar .TH PAIRALIGN "1" "September 2009" "Version 1.0 (15. July 2009) Revision: 4566" "User Commands" .SH NAME pair_align \- Pairwise alignment .SH SYNOPSIS .B pair_align \fI-s \fR[\fIOptions\fR] .SH DESCRIPTION Pairwise alignment \- PairAlign .TP \fB\-h\fR, \fB\-\-help\fR displays this help message .TP \fB\-V\fR, \fB\-\-version\fR print version information .SS "Main Options:" .TP \fB\-s\fR, \fB\-\-seq\fR file with 2 sequences .TP \fB\-a\fR, \fB\-\-alphabet\fR [protein | dna | rna] sequence alphabet (default protein) .TP \fB\-m\fR, \fB\-\-method\fR [nw, gotoh, sw, lcs] alignment method (default gotoh) nw = Needleman\-Wunsch gotoh = Gotoh sw = Smith\-Waterman lcs = Longest common subsequence .TP \fB\-o\fR, \fB\-\-outfile\fR output filename (default out.fasta) .TP \fB\-f\fR, \fB\-\-format\fR [fasta | msf] output format (default fasta) .SS "Scoring Options:" .TP \fB\-g\fR, \fB\-\-gop\fR gap open penalty (default \fB\-11\fR) .TP \fB\-e\fR, \fB\-\-gex\fR gap extension penalty (default \fB\-1\fR) .TP \fB\-ma\fR, \fB\-\-matrix\fR score matrix (default Blosum62) .TP \fB\-ms\fR, \fB\-\-msc\fR match score (default 5) .TP \fB\-mm\fR, \fB\-\-mmsc\fR mismatch penalty (default \fB\-4\fR) .SS "Banded Alignment Options:" .TP \fB\-lo\fR, \fB\-\-low\fR lower diagonal .TP \fB\-hi\fR, \fB\-\-high\fR upper diagonal .SS "DP Matrix Configuration Options:" .TP \fB\-c\fR, \fB\-\-config\fR [ffff | ... | tttt] alignment configuration (default ffff) tfff = First row with 0's ftff = First column with 0's fftf = Search last column for max ffft = Search last row for max All combinations are allowed. .SH AUTHOR .br pair_align was written by Tobias Rausch. .PP This manual page was generated using html2man and polished by Soeren Sonnenburg , for the Debian project (but may be used by others). debian/tree_recon.10000644000000000000000000000240711261043504011374 0ustar .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.36. .TH VERSION "1" "September 2009" "Version 1.01 (18. August 2009) Revision: 4692" "User Commands" .SH NAME Version \- Tree reconstrucion .SH SYNOPSIS .B tree_recon \fI-m \fR[\fIOptions\fR] .SH DESCRIPTION Tree reconstrucion \- TreeRecon .TP \fB\-h\fR, \fB\-\-help\fR displays this help message .TP \fB\-V\fR, \fB\-\-version\fR print version information .SS "Main Options:" .TP \fB\-m\fR, \fB\-\-matrix\fR file with distance matrix At least 3 species required. .TP \fB\-b\fR, \fB\-\-build\fR [nj, min, max, avg, wavg] tree building method (default nj) \fR nj = Neighbor\-joining \fR min = UPGMA single linkage \fR max = UPGMA complete linkage \fR avg = UPGMA average linkage \fR wavg = UPGMA weighted average linkage .IP Neighbor\-joining creates an unrooted tree. We root that tree at the last joined pair. .TP \fB\-o\fR, \fB\-\-outfile\fR output filename (default tree.dot) .TP \fB\-f\fR, \fB\-\-format\fR [dot | newick] output format (default dot) .SH AUTHOR .br tree_recon was written by Tobias Rausch. .PP This manual page was generated using html2man and polished by Soeren Sonnenburg , for the Debian project (but may be used by others). debian/dfi.10000644000000000000000000000242111261043504010005 0ustar .TH DFI "1" "September 2009" "DFI version 2.0 20090715 [4670]" "User Commands" .SH NAME DFI \- The Deferred Frequency Index .SH SYNOPSIS .B dfi [\fIOPTION\fR]... \fI--minmax \fR... \fI--minmax \fR .SH DESCRIPTION DFI \- The Deferred Frequency Index .TP dfi [OPTION]... \fB\-\-growth\fR .TP dfi [OPTION]... \fB\-\-entropy\fR ... .TP \fB\-h\fR, \fB\-\-help\fR displays this help message .TP \fB\-V\fR, \fB\-\-version\fR print version information .TP \fB\-f\fR, \fB\-\-minmax\fR NUM1 NUM2 solve Frequent Pattern Mining Problem .TP \fB\-g\fR, \fB\-\-growth\fR NUM1 NUM2 solve Emerging Substring Mining Problem .TP \fB\-e\fR, \fB\-\-entropy\fR NUM1 NUM2 solve Entropy Mining Problem .TP \fB\-p\fR, \fB\-\-protein\fR use AminoAcid alphabet (for proteomes) .TP \fB\-d\fR, \fB\-\-dna\fR use DNA alphabet (for genomes) .TP \fB\-m\fR, \fB\-\-maximal\fR output only left and right maximal substrings The default is byte alphabet .SH AUTHOR .br dfi was written by David Weese and Marcel H. Schulz. .PP This manual page was generated using html2man and polished by Soeren Sonnenburg , for the Debian project (but may be used by others). debian/source/0000755000000000000000000000000011745241411010466 5ustar debian/source/format0000644000000000000000000000001411301174376011677 0ustar 3.0 (quilt) debian/seqan-dev.install0000644000000000000000000000007111745324352012445 0ustar docs/* usr/share/doc/seqan-dev/html seqan usr/include debian/compat0000644000000000000000000000000211632362363010371 0ustar 8 debian/orig-tar.sh0000755000000000000000000000072411745241012011251 0ustar #!/bin/sh set -e SEQANDIR=seqan-$2 SEQANFILE=seqan_${2}.orig.tar.xz # called by uscan with '--upstream-version' mkdir $SEQANDIR echo $3 unzip -q $3 # -d $SEQANDIR rm -rf $SEQANDIR/lib/samtools tar cJf $SEQANFILE $SEQANDIR rm -rf $SEQANDIR rm -f $3 # move to directory 'tarballs' if [ -r .svn/deb-layout ]; then . .svn/deb-layout else origDir=../tarballs fi mkdir -p $origDir mv $SEQANFILE $origDir echo "moved $SEQANFILE to $origDir" exit 0 debian/patches/0000755000000000000000000000000011745241411010615 5ustar debian/patches/series0000644000000000000000000000001711636037220012030 0ustar samtools.patch debian/patches/samtools.patch0000644000000000000000000000106011636037220013474 0ustar Description: Corrects path to SAMtools headers in Debian. Origin: vendor Forwarded: no Not checked yet it if it still relevant for next upstream release. diff --git a/seqan/store.h b/seqan/store.h index b558e94..de54ace 100644 --- a/seqan/store.h +++ b/seqan/store.h @@ -47,8 +47,8 @@ #endif // #ifndef SEQAN_HAS_SAMTOOLS #if SEQAN_HAS_SAMTOOLS -#include -#include +#include +#include #endif // #if SEQAN_HAS_SAMTOOLS ////////////////////////////////////////////////////////////////////////////// debian/seqan-apps.manpages0000644000000000000000000000020311261043504012742 0ustar debian/dfi.1 debian/micro_razers.1 debian/pair_align.1 debian/razers.1 debian/seqan_tcoffee.1 debian/seqcons.1 debian/tree_recon.1 debian/micro_razers.10000644000000000000000000000430111261043504011741 0ustar .TH MICRORAZERS "1" "September 2009" "MicroRazerS version 0.1 20090710 (prerelease)" "User Commands" .SH NAME MicroRazerS \- Rapid Alignment of Small RNA Reads .SH SYNOPSIS .B micro_razers [\fIOPTION\fR]... \fI \fR .SH DESCRIPTION MicroRazerS \- Rapid Alignment of Small RNA Reads .SS "Main Options:" .TP \fB\-o\fR, \fB\-\-output\fR FILE change output filename (default .result) .TP \fB\-sL\fR, \fB\-\-seed\-length\fR NUM seed length (default 16) .TP \fB\-sE\fR, \fB\-\-seed\-error\fR allow for one error in the seed (default off) .TP \fB\-rr\fR, \fB\-\-recognition\-rate\fR set lower bound of sensitivity level for one\-error matches (default 100) .TP \fB\-f\fR, \fB\-\-forward\fR only compute forward matches .TP \fB\-r\fR, \fB\-\-reverse\fR only compute reverse complement matches .TP \fB\-mN\fR, \fB\-\-match\-N\fR \&'N' matches with all other characters .TP \fB\-m\fR, \fB\-\-max\-hits\fR NUM output only NUM of the best hits (default 100) .TP \fB\-pa\fR, \fB\-\-purge\-ambiguous\fR purge reads with more than max\-hits best matches .TP \fB\-lm\fR, \fB\-\-low\-memory\fR may decrease memory usage at the expense of runtime .TP \fB\-v\fR, \fB\-\-verbose\fR verbose mode .TP \fB\-vv\fR, \fB\-\-vverbose\fR very verbose mode .TP \fB\-V\fR, \fB\-\-version\fR print version number .TP \fB\-h\fR, \fB\-\-help\fR print this help .SS "Output Format Options:" .TP \fB\-a\fR, \fB\-\-alignment\fR dump the alignment for each match .TP \fB\-gn\fR, \fB\-\-genome\-naming\fR NUM select how genomes are named 0 = use Fasta id (default) 1 = enumerate beginning with 1 .TP \fB\-rn\fR, \fB\-\-read\-naming\fR NUM select how reads are named 0 = use Fasta id (default) 1 = enumerate beginning with 1 2 = use the read sequence (only for short reads!) .TP \fB\-so\fR, \fB\-\-sort\-order\fR NUM select how matches are sorted 0 = 1. read number, 2. genome position (default) 1 = 1. genome position, 2. read number .TP \fB\-pf\fR, \fB\-\-position\-format\fR 0 = gap space (default) 1 = position space .SH AUTHOR .br MicroRazerSwas written by Anne-Katrin Emde. .PP This manual page was generated using html2man and polished by Soeren Sonnenburg , for the Debian project (but may be used by others). debian/rules0000755000000000000000000000336611745344300010257 0ustar #!/usr/bin/make -f include /usr/share/cdbs/1/rules/debhelper.mk include /usr/share/cdbs/1/class/cmake.mk DEB_SRCDIR := cmake DEB_MAKE_INSTALL_TARGET := DEB_DH_BUILDDEB_ARGS = -- -Zxz ## dh does not seem to propagate the correct options to cmake configure step #%: # dh $@ --parallel --buildsystem=cmake #override_dh_auto_build: makebuilddir:: # create backups of original *generated_forwards.h files to build twice in a row for header in `find seqan -name "*generated_forwards.h"` ; do \ mkdir -p orig/`dirname $$header` ; \ cp -a $$header orig/$${header} ; \ done # dh_auto_build #override_dh_auto_install: # dh_auto_install install/seqan-apps:: debian/stamp-install-seqan-apps debian/stamp-install-seqan-apps: #install binaries for APP in `find $(CURDIR)/obj*/apps -mindepth 1 -maxdepth 1 -executable -type f` ; do \ cp -a $$APP $(CURDIR)/debian/seqan-apps/usr/lib/sequan/bin/ ; done #install readmes for APP in `find apps -name README` ; do \ app=`echo $$APP | sed 's?.*apps/\(.\+\)/README?\1?'` ; \ echo $$app ; \ cp -a $$APP $(CURDIR)/debian/seqan-apps/usr/share/doc/seqan-apps/README.$$app ; \ done # Delete extra license files install/seqan-dev:: @echo "This should be post-install action after installing files for seqan-dev ... but the doc is lying :-(" find debian -type f -name LICENSE -delete # FIXME: Anybody able to convince cdbs to do what the doc is promising and remove the unneeded LICENSE files? #override_dh_auto_clean: # dh_auto_clean clean:: if [ -d orig ] ; then \ for header in `find orig -name "*generated_forwards.h"` ; do \ mv $${header} `echo $$header | sed 's?orig/??'` ; \ done ; \ fi rm -rf orig get-orig-source: uscan --force-download @echo successfully retrieved upstream tarball debian/reference0000644000000000000000000000061111211672057011047 0ustar @Article{18184432, AUTHOR = {Doring, Andreas and Weese, David and Rausch, Tobias and Reinert, Knut}, TITLE = {SeqAn An efficient, generic C++ library for sequence analysis}, JOURNAL = {BMC Bioinformatics}, VOLUME = {9}, YEAR = {2008}, NUMBER = {1}, PAGES = {11}, URL = {http://www.biomedcentral.com/1471-2105/9/11}, DOI = {10.1186/1471-2105-9-11}, PubMedID = {18184432}, ISSN = {1471-2105}, } debian/seqan_tcoffee.10000644000000000000000000000471611261043504012056 0ustar .TH SEQAN_TCOFFEE "1" "September 2009" "Version 1.11 (30. July 2009) Revision: 4637" "User Commands" .SH NAME seqan_tcoffee \- Multiple sequence alignment .SH SYNOPSIS .B seqan_tcoffee \fI-s \fR[\fIOptions\fR] .SH DESCRIPTION Multiple sequence alignment \- SeqAn::T\-Coffee .TP \fB\-h\fR, \fB\-\-help\fR displays this help message .TP \fB\-V\fR, \fB\-\-version\fR print version information .SS "Main Options:" .TP \fB\-s\fR, \fB\-\-seq\fR file with sequences .TP \fB\-a\fR, \fB\-\-alphabet\fR [protein | dna | rna] sequence alphabet (default protein) .TP \fB\-o\fR, \fB\-\-outfile\fR output filename (default out.fasta) .TP \fB\-f\fR, \fB\-\-format\fR [fasta | msf] output format (default fasta) .SS "Segment Match Generation Options:" .TP \fB\-m\fR, \fB\-\-method\fR list of match generation methods \fR global = Global alignments \fR local = Local alignments \fR overlap = Overlap alignments \fR lcs = Longest common subsequence \fR Default: global,local \IP No spaces in\-between. .TP \fB\-bl\fR, \fB\-\-blast\fR ,,... list of BLAST match files .TP \fB\-mu\fR, \fB\-\-mummer\fR ,,... list of MUMmer match files .TP \fB\-al\fR, \fB\-\-aln\fR ,,... list of FASTA align files .TP \fB\-li\fR, \fB\-\-lib\fR ,,... list of T\-Coffee libraries .SS "Scoring Options:" .TP \fB\-g\fR, \fB\-\-gop\fR gap open penalty (default \fB\-13\fR) .TP \fB\-e\fR, \fB\-\-gex\fR gap extension penalty (default \fB\-1\fR) .TP \fB\-ma\fR, \fB\-\-matrix\fR score matrix (default Blosum62) .TP \fB\-ms\fR, \fB\-\-msc\fR match score (default 5) .TP \fB\-mm\fR, \fB\-\-mmsc\fR mismatch penalty (default \fB\-4\fR) .SS "Guide Tree Options:" .TP \fB\-u\fR, \fB\-\-usetree\fR tree filename .TP \fB\-b\fR, \fB\-\-build\fR [nj, min, max, avg, wavg] tree building method (default nj) \fR nj = Neighbor\-joining \fR min = UPGMA single linkage \fR max = UPGMA complete linkage \fR avg = UPGMA average linkage \fR wavg = UPGMA weighted average linkage .IP Neighbor\-joining creates an unrooted tree. We root that tree at the last joined pair. .SS "Alignment Evaluation Options:" .TP \fB\-i\fR, \fB\-\-infile\fR alignment file .SH AUTHOR .br seqan_tcoffee was written by Tobias Rausch. .PP This manual page was generated using html2man and polished by Soeren Sonnenburg , for the Debian project (but may be used by others). debian/seqan-dev.doc-base0000644000000000000000000000205111745335666012466 0ustar Document: seqan-dev Title: SeqAn - The Library for Sequence Analysis Author: Andreas Döring David Weese Tobias Rausch Stephan Aiche Anne-Katrin Emde Carsten Kemena Konrad Ludwig Moritz Rudolph Marcel H. Schulz. Abstract: SeqAn - The Library for Sequence Analysis SeqAn is the open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. SeqAn applies a unique generic design that guarantees high performance, generality, extensibility, and integration with other libraries. SeqAn is easy to use and simplifies the development of new software tools with a minimal loss of performance. Section: Science/Biology Format: html Files: /usr/share/doc/seqan-dev/html/* Index: /usr/share/doc/seqan-dev/html/index.html debian/seqan-apps.dirs0000644000000000000000000000005411745252354012130 0ustar usr/share/doc/seqan-apps usr/lib/sequan/bin debian/seqan-apps.links0000644000000000000000000000051411745245060012304 0ustar usr/lib/sequan/bin/dfi usr/bin/dfi usr/lib/sequan/bin/micro_razers usr/bin/micro_razers usr/lib/sequan/bin/pair_align usr/bin/pair_align usr/lib/sequan/bin/razers usr/bin/razers usr/lib/sequan/bin/seqan_tcoffee usr/bin/seqan_tcoffee usr/lib/sequan/bin/seqcons usr/bin/seqcons usr/lib/sequan/bin/tree_recon usr/bin/tree_recon debian/control0000644000000000000000000000344111745336202010576 0ustar Source: seqan Section: science Priority: optional Maintainer: Debian Med Packaging Team Uploaders: Soeren Sonnenburg , Andreas Tille Build-Depends: cdbs, debhelper (>= 8), cmake, zlib1g-dev, libbam-dev, libboost-dev Standards-Version: 3.9.3 Homepage: http://www.seqan.de/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/seqan/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/seqan/trunk/ Package: seqan-apps Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: C++ library for the analysis of biological sequences SeqAn is a C++ template library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. This library applies a unique generic design that guarantees high performance, generality, extensibility, and integration with other libraries. SeqAn is easy to use and simplifies the development of new software tools with a minimal loss of performance. This package contains the applications dfi, pair_align, micro_razers, seqan_tcoffee, seqcons, razers and tree_recon. Package: seqan-dev Section: libdevel Architecture: all Depends: ${shlibs:Depends}, ${misc:Depends} Description: C++ library for the analysis of biological sequences (development) SeqAn is a C++ template library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. This library applies a unique generic design that guarantees high performance, generality, extensibility, and integration with other libraries. SeqAn is easy to use and simplifies the development of new software tools with a minimal loss of performance. . This package contains the developer files, documentation and examples. debian/seqan-dev.docs0000644000000000000000000000000611745242054011723 0ustar demos debian/seqcons.10000644000000000000000000000331411261043504010720 0ustar .TH SEQCONS "1" "September 2009" "Version 0.22 (06. August 2009) Revision: 4663" "User Commands" .SH NAME seqcons \- Multi\-read alignment .SH SYNOPSIS .B seqcons \fI-r \fR[\fIOptions\fR] .SH DESCRIPTION Multi\-read alignment \- SeqCons .IP seqcons \fB\-a\fR [Options] .TP \fB\-h\fR, \fB\-\-help\fR displays this help message .TP \fB\-V\fR, \fB\-\-version\fR print version information .SS "Main Options:" .TP \fB\-r\fR, \fB\-\-reads\fR file with reads .TP \fB\-a\fR, \fB\-\-afg\fR message file .TP \fB\-o\fR, \fB\-\-outfile\fR output filename (default align.txt) .TP \fB\-f\fR, \fB\-\-format\fR [seqan | afg] output format (default afg) .TP \fB\-m\fR, \fB\-\-method\fR [realign | msa] alignment method (default realign) .TP \fB\-b\fR, \fB\-\-bandwidth\fR bandwidth (default 8) .TP \fB\-n\fR, \fB\-\-noalign\fR no align, only convert input .SS "MSA Method Options:" .TP \fB\-ma\fR, \fB\-\-matchlength\fR min. overlap length (default 15) .TP \fB\-qu\fR, \fB\-\-quality\fR min. overlap precent identity (default 80) .TP \fB\-ov\fR, \fB\-\-overlaps\fR min. number of overlaps per read (default 3) .TP \fB\-wi\fR, \fB\-\-window\fR window size (default 0) /*If this parameter is > 0 then all .IP overlaps within a given window are computed.*/ .SS "ReAlign Method Options:" .TP \fB\-in\fR, \fB\-\-include\fR include contig sequence .TP \fB\-rm\fR, \fB\-\-rmethod\fR [nw | gotoh] realign method (default gotoh) .SH AUTHOR .br seqcons was written by Tobias Rausch .PP This manual page was generated using html2man and polished by Soeren Sonnenburg , for the Debian project (but may be used by others). debian/upstream0000644000000000000000000000114611717653703010765 0ustar Contact: SeqAn Team (http://www.seqan.de/contact-us.html) Reference-DOI: 10.1186/1471-2105-9-11 Donate: http://www.seqan.de/ Homepage: http://www.seqan.de/ Name: SeqAn Reference-PMID: 18184432 Reference: AUTHOR: Doring, Andreas and Weese, David and Rausch, Tobias and Reinert, Knut TITLE: SeqAn An efficient, generic C++ library for sequence analysis JOURNAL: BMC Bioinformatics VOLUME: 9 YEAR: 2008 NUMBER: 1 PAGES: 11 URL: http://www.biomedcentral.com/1471-2105/9/11 ISSN: 1471-2105 Watch: | http://www.seqan.de/downloads/releases.html \ .*/Seqan_Release_([\d\.]+).zip \ debian debian/orig-tar.sh