debian/0000755000000000000000000000000011736555443007203 5ustar debian/upstream0000644000000000000000000000160311736554114010760 0ustar Contact: Timo Lassmann Name: Kalign Homepage: http://msa.sbc.su.se/ Reference: - Author: Lassmann, Timo and Frings, Oliver and Sonnhammer, Erik L. L. Title: "Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features" Journal: Nucl. Acids Res. Volume: 37 Number: 3 Pages: 858-865 Year: 2009 DOI: 10.1093/nar/gkn1006 PMID: 19103665 URL: http://nar.oxfordjournals.org/cgi/content/abstract/37/3/858 - Authors: Lassmann, Timo and Sonnhammer, Erik L. L. Title: Kalign--an accurate and fast multiple sequence alignment algorithm Journal: BMC Bioinformatics Volume: 6 Number: 1 Pages: 298 Year: 2005 DOI: 10.1186/1471-2105-6-298 PMID: 16343337 URL: http://www.biomedcentral.com/1471-2105/6/298 eprint: http://www.biomedcentral.com/content/pdf/1471-2105-6-298.pdf Watch: NA debian/source/0000755000000000000000000000000011736553676010511 5ustar debian/source/format0000644000000000000000000000001411606404406011675 0ustar 3.0 (quilt) debian/docs0000644000000000000000000000000711262651516010043 0ustar README debian/kalign.bash_completion0000644000000000000000000000256011262652463013535 0ustar # -*- mode: shell-script; sh-basic-offset: 8; indent-tabs-mode: t -*- # ex: ts=8 sw=8 noet filetype=sh # # kalign(1) completion # have kalign && { _kalign() { local cur prev COMPREPLY=() cur=`_get_cword` prev=${COMP_WORDS[COMP_CWORD-1]} case "$prev" in -@(i|input|infile|in|o|output|outfile|out)) _filedir return 0 ;; -@(c|sort)) COMPREPLY=( $( compgen -W "input tree gaps" -- "$cur" ) ) return 0 ;; -@(g|feature)) # TODO: finish this list! COMPREPLY=( $( compgen -W "all maxplp STRUCT PFAM-A" -- "$cur" ) ) return 0 ;; -@(d|distance)) COMPREPLY=( $( compgen -W "wu pair" -- "$cur" ) ) return 0 ;; -@(b|guide_tree|tree)) COMPREPLY=( $( compgen -W "nj upgma" -- "$cur" ) ) return 0 ;; -@(f|format)) COMPREPLY=( $( compgen -W "fasta msf aln clu macsim" -- "$cur" ) ) return 0 ;; esac if [[ "$cur" == -* ]]; then COMPREPLY=( $( compgen -W "-s -gapopen -gap_open -gpo \ -e -gapextension -gap_ext -gpe \ -t -terminal_gap_extension_penalty -tgpe \ -m -matrix_bonus -bonus \ -c -sort \ -g -feature -same_feature_score -diff_feature_score \ -d -distance \ -b -guide-tree -tree \ -z -zcutoff \ -i -input -infile -in \ -o -output -outfile -out \ -a -gap_inc \ -f -format \ -q -quiet" \ -- "$cur" ) ) else _filedir fi return 0 } complete -F _kalign $filenames kalign } debian/copyright0000644000000000000000000000307011736555217011135 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: Kalign Upstream-Contact: Oliver Frings Source: http://msa.cgb.ki.se/downloads/kalign/current.tar.gz Files: * Copyright: © 2004–2008 Timo Lassmann © 2008-2011 Timo Lassmann , Oliver Frings License: GPL-2+ Files: debian/* Copyright: © 2006–2011 Charles Plessy © 2008 David Paleino © 2008-2012 Andreas Tille License: GPL-2+ Files: debian/kalign.1* Copyright: © 2006–2009 Charles Plessy License: GPL-2+ License: GPL-2+ This package 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 package 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 package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA . On Debian systems, the complete text of the GNU General Public License version 2 can be found in ‘/usr/share/common-licenses/GPL-2’. debian/compat0000644000000000000000000000000211736555434010401 0ustar 9 debian/install0000644000000000000000000000002011262651437010556 0ustar kalign usr/bin debian/control0000644000000000000000000000206011736555443010604 0ustar Source: kalign Section: science Priority: optional Maintainer: Debian Med Packaging Team DM-Upload-Allowed: yes Uploaders: Charles Plessy , Andreas Tille Build-Depends: debhelper (>= 9) Standards-Version: 3.9.3 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/kalign/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/kalign/trunk/ Homepage: http://msa.sbc.su.se/ Package: kalign Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Enhances: t-coffee, bioperl-run Description: Global and progressive multiple sequence alignment Kalign is a command line tool to perform multiple alignment of biological sequences. It employs the Muth-Manber string-matching algorithm, to improve both the accuracy and speed of the alignment. It uses global, progressive alignment approach, enriched by employing an approximate string-matching algorithm to calculate sequence distances and by incorporating local matches into the otherwise global alignment. debian/manpages0000644000000000000000000000002011262651457010705 0ustar debian/kalign.1 debian/reference0000644000000000000000000000152411151451510011043 0ustar @article{TimoLassmann02012009, author = {Lassmann, Timo and Frings, Oliver and Sonnhammer, Erik L. L.}, title = {{Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features}}, journal = {Nucl. Acids Res.}, volume = {37}, number = {3}, pages = {858-865}, doi = {10.1093/nar/gkn1006}, year = {2009}, URL = {http://nar.oxfordjournals.org/cgi/content/abstract/37/3/858}, eprint = {http://nar.oxfordjournals.org/cgi/reprint/37/3/858.pdf} } @Article{16343337, AUTHOR = {Lassmann, Timo and Sonnhammer, Erik}, TITLE = {Kalign - an accurate and fast multiple sequence alignment algorithm}, JOURNAL = {BMC Bioinformatics}, VOLUME = {6}, YEAR = {2005}, NUMBER = {1}, PAGES = {298}, URL = {http://www.biomedcentral.com/1471-2105/6/298}, DOI = {10.1186/1471-2105-6-298}, PubMedID = {16343337}, ISSN = {1471-2105}, } debian/watch0000644000000000000000000000023311736544671010233 0ustar # There is no more version number: http://msa.sbc.su.se/downloads/kalign/current.tar.gz #version=3 #http://msa.cgb.ki.se/downloads/ kalign-?(\d).(\d+).tgz debian/changelog0000644000000000000000000000711311736555430011053 0ustar kalign (1:2.03+20110620-2) unstable; urgency=low [ Charles Plessy ] * renamed debian/upstream-metadata.yaml to debian/upstream [ Andreas Tille ] * debian/upstream: - Added another citation from tasks file - Fixed Homepage * debian/source/format: 3.0 (quilt) * debian/watch: Fixed hint to download URL * debian/control: - Fixed Homepage - Standards-Version: 3.9.3 (no changes needed) * debian/copyright: Fixed DEP5 issues and verified using cme fix dpkg-copyright * debhelper 9 (control+compat) -- Andreas Tille Thu, 29 Mar 2012 15:28:43 +0200 kalign (1:2.03+20110620-1) unstable; urgency=low * New upstream release. Using 2.04 as a version number was a mistake of mine, it should have been called 2.03+20081031 as Upstream sometimes updates the source archive ‘current.tar.gz’ without incrementing the version number. * Collected information about Upstream in ‘debian/upstream-metadata.yaml’. * Using Debhelper 8 (debian/compat, debian/control). * Corrected VCS information in debian/control. * Enhances: bioperl-run, that has a kalign wrapper (debian/control). * Incremented Standards-Version to reflect conformance with Policy 3.9.2. (debian/control, no changes needed). -- Charles Plessy Sat, 25 Jun 2011 17:23:01 +0900 kalign (2.04-2) unstable; urgency=low [ David Paleino ] * Removed myself from Uploaders [ Andreas Tille ] * debian/control: - Standards-Version: 3.8.3 - debhelper (>= 7.1) to use override facility * debian/rules: - removed code to create manpage - just keep the created one - short rules file using dh * debian/watch: - deactivated; upstream does not seem to respond to our request to enable versioned tarballs - so the watch file makes no sense Closes: #456479 * Applied patch to enable bash completion. Thanks to David Paleino Closes: #446047 -- Andreas Tille Tue, 06 Oct 2009 16:21:45 +0200 kalign (2.04-1) unstable; urgency=low * New upstream release. * debian/copyright made machine-readable. * debian/rules: replaced deprecated dh_clean -k by dh_prep. * debian/control: - Updated my email address (debian/control). - Checked compliance with Policy 3.8.0 (no changes needed). - Using debhelper 7 (also in debian/compat). - Upadated description and moved reference to debian/reference. * debian/kalign.1*: updated the manual pages. -- Charles Plessy Thu, 26 Feb 2009 00:19:44 +0900 kalign (2.03-2) unstable; urgency=low [ Charles Plessy ] * debian/control: - Add Subversion repository URL to debian/control. - Moved the Homepage: field out from the package's description. - Enhances: t-coffee. [ David Paleino ] * debian/kalign.1 added - manpages are now statically generated * debian/control: - B-D updated (see above) - added myself to Uploaders - moved XS-Vcs-* fields to Vcs-* * debian/rules: - reflecting static build of manpages - minor changes * Updated to Standards-Version 3.7.3 (no changes needed) [ Andreas Tille ] * Added myself to Uploaders -- Andreas Tille Tue, 18 Mar 2008 09:54:17 +0100 kalign (2.03-1) unstable; urgency=low * New upstream release. * Mended the watch file. * Updated the manpage. -- Charles Plessy Wed, 21 Feb 2007 09:07:33 +0900 kalign (1.04-1) unstable; urgency=low * Initial release Closes: #365344 -- Charles Plessy Sat, 29 Apr 2006 23:02:57 +0900 debian/rules0000755000000000000000000000036111262655747010265 0ustar #!/usr/bin/make -f # -*- makefile -*- # Build rules for the Debian package kalign pkg:=kalign %: dh $@ override_dh_auto_install: install -D -m u=rw,go=r debian/$(pkg).bash_completion $(CURDIR)/debian/$(pkg)/etc/bash_completion.d/$(pkg) debian/kalign.10000644000000000000000000000775711151451510010527 0ustar .\" Title: KALIGN .\" Author: Timo Lassmann .\" Generator: DocBook XSL Stylesheets v1.73.2 .\" Date: February 25, 2009 .\" Manual: Kalign User Manual .\" Source: kalign 2.04 .\" .TH "KALIGN" "1" "February 25, 2009" "kalign 2.04" "Kalign User Manual" .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .SH "NAME" kalign \- performs multiple alignment of biological sequences. .SH "SYNOPSIS" .HP 7 \fBkalign\fR [\fIinfile\&.fasta\fR] [\fIoutfile\&.fasta\fR] [Options] .HP 7 \fBkalign\fR [\-i\ \fIinfile\&.fasta\fR] [\-o\ \fIoutfile\&.fasta\fR] [Options] .HP 7 \fBkalign\fR [<\ \fIinfile\&.fasta\fR] [>\ \fIoutfile\&.fasta\fR] [Options] .SH "DESCRIPTION" .PP \fBKalign\fR is a command line tool to perform multiple alignment of biological sequences\&. It employs the Muth?Manber string\-matching algorithm, to improve both the accuracy and speed of the alignment\&. It uses global, progressive alignment approach, enriched by employing an approximate string\-matching algorithm to calculate sequence distances and by incorporating local matches into the otherwise global alignment\&. .SH "OPTIONS" .PP \fB\-s\fR \fB\-gpo\fR \fB\-gapopen\fR \fB\-gap_open\fR \fIx\fR .RS 4 Gap open penalty \&. .RE .PP \fB\-e\fR \fB\-gpe\fR \fB\-gap_ext\fR \fB\-gapextension\fR \fIx\fR .RS 4 Gap extension penalty\&. .RE .PP \fB\-t\fR \fB\-tgpe\fR \fB\-terminal_gap_extension_penalty\fR \fIx\fR .RS 4 Terminal gap penalties\&. .RE .PP \fB\-m\fR \fB\-bonus\fR \fB\-matrix_bonus\fR \fIx\fR .RS 4 A constant added to the substitution matrix\&. .RE .PP \fB\-c\fR \fB\-sort\fR \fI\fR .RS 4 The order in which the sequences appear in the output alignment\&. .RE .PP \fB\-g\fR \fB\-feature\fR .RS 4 Selects feature mode and specifies which features are to be used: e\&.g\&. all, maxplp, STRUCT, PFAM\-A? .RE .PP \fB\-same_feature_score\fR .RS 4 Score for aligning same features\&. .RE .PP \fB\-diff_feature_score\fR .RS 4 Penalty for aligning different features\&. .RE .PP \fB\-d\fR \fB\-distance\fR \fI\fR .RS 4 Distance method .RE .PP \fB\-b\fR \fB\-tree\fR \fB\-guide\-tree\fR \fI\fR .RS 4 Guide tree method\&. .RE .PP \fB\-z\fR \fB\-zcutoff\fR .RS 4 Parameter used in the wu\-manber based distance calculation\&. .RE .PP \fB\-i\fR \fB\-in\fR \fB\-input\fR .RS 4 Name of the input file\&. .RE .PP \fB\-o\fR \fB\-out\fR \fB\-output\fR .RS 4 Name of the output file\&. .RE .PP \fB\-a\fR \fB\-gap_inc\fR .RS 4 Increases gap penalties depending on the number of existing gaps\&. .RE .PP \fB\-f\fR \fB\-format\fR \fI\fR .RS 4 The output format\&. .RE .PP \fB\-q\fR \fB\-quiet\fR .RS 4 Print nothing to STDERR\&. Read nothing from STDIN\&. .RE .SH "REFERENCES" .sp .RS 4 \h'-04'\(bu\h'+03'Timo Lassmann and Erik L\&.L\&. Sonnhammer (2005) Kalign \- an accurate and fast multiple sequence alignment algorithm\&. BMC Bioinformatics 6:298 .RE .sp .RS 4 \h'-04'\(bu\h'+03'Timo Lassmann, Oliver Frings and Erik L\&. L\&. Sonnhammer (2009) Kalign2: high\-performance multiple alignment of protein and nucleotide sequences allowing external features\&. Nucleic Acid Research 3:858?865\&. .RE .SH "AUTHORS" .PP \fBTimo Lassmann\fR <\&timolassmann@gmail\&.com\&> .sp -1n .IP "" 4 Upstream author of Kalign\&. .PP \fBCharles Plessy\fR <\&plessy@debian\&.org\&> .sp -1n .IP "" 4 Wrote the manpage\&. .SH "COPYRIGHT" Copyright \(co 2004, 2005, 2006, 2007, 2008 Timo Lassmann .br .PP Kalign 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\&. .PP This manual page was written by Charles Plessy for the Debian(TM) system (but may be used by others)\&. Permission is granted to copy, distribute and/or modify this document under the same terms as kalign itself\&. .PP On Debian systems, the complete text of the GNU General Public License version 2 can be found in \fI/usr/share/common\-licenses/GPL\-2\fR\&. .sp