debian/0000755000000000000000000000000012140534516007167 5ustar debian/control0000644000000000000000000000254512140530450010571 0ustar Source: proalign Section: science Priority: optional Maintainer: Debian Med Packaging Team DM-Upload-Allowed: yes Uploaders: Andreas Tille , Thorsten Alteholz Build-Depends: debhelper (>= 9), default-jdk Standards-Version: 3.9.4 Homepage: http://ueg.ulb.ac.be/ProAlign/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/proalign/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/proalign/trunk/ Package: proalign Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, default-jre Description: Probabilistic multiple alignment program ProAlign performs probabilistic sequence alignments using hidden Markov models (HMM). It includes a graphical interface (GUI) allowing to (i) perform alignments of nucleotide or amino-acid sequences, (ii) view the quality of solutions, (iii) filter the unreliable alignment regions and (iv) export alignments to other software. . ProAlign uses a progressive method, such that multiple alignment is created stepwise by performing pairwise alignments in the nodes of a guide tree. Sequences are described with vectors of character probabilities, and each pairwise alignment reconstructs the ancestral (parent) sequence by computing the probabilities of different characters according to an evolutionary model. debian/manifest.txt0000644000000000000000000000006512140264124011532 0ustar Manifest-version: 1.0 Main-Class: proalign.ProAlign debian/proalign.install0000644000000000000000000000010712140263760012370 0ustar debian/scripts/proalign usr/bin build/ProAlign.jar usr/share/proalign debian/copyright0000644000000000000000000000231511761613477011137 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: ProAlign Upstream-Contact: Ari Löytynoja & Michel C. Milinkovitch Source: http://ueg.ulb.ac.be/ProAlign/ Files: * Copyright: © 2002-2003 Ari Löytynoja and Michel C. Milinkovitch. License: GPL-2+ Files: debian/* Copyright: © 2012 Andreas Tille License: GPL-2+ 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 package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA . On Debian systems, the full text of the GNU General Public License version 2 can be found in the file `/usr/share/common-licenses/GPL-2'. debian/changelog0000644000000000000000000000023512140534444011041 0ustar proalign (0.603-1) unstable; urgency=low * Initial release (Closes: #378290) -- Thorsten Alteholz Tue, 01 May 2013 18:00:00 +0200 debian/compat0000644000000000000000000000000211761613477010401 0ustar 9 debian/scripts/0000755000000000000000000000000012140534516010656 5ustar debian/scripts/proalign0000644000000000000000000000076612140477306012430 0ustar #!/bin/sh PARA=$@ if [ -z $JAVA_HOME ]; then java=java else java=$JAVA_HOME/bin/java fi if [ -x /usr/share/proalign ]; then if [ -r /usr/share/proalign/ProAlign.jar ]; then #cd /usr/share/proalign && $java -jar ProAlign.jar $java -jar /usr/share/proalign/ProAlign.jar $PARA else echo "Could not find /usr/share/proalign/ProAlign.jar" fi else echo "Could not find /usr/share/proalign directory." fi debian/proalign.10000644000000000000000000000335112140500371011056 0ustar .TH PROALIGN "1" "May 2013" "ProAlign" "User Commands" .SH NAME proalign \- a probabilistic multiple alignment program .SH SYNOPSIS .B proalign [OPTIONS] .SH DESCRIPTION Only limited usage of the program is possible from command line. Better use version with GUI (start without OPTIONS). .SH OPTIONS .TP \fB\-nogui\fR force command line .TP \fB-seqfile=\fR .TP \fB-treefile=\fR .TP \fB-newtree \fR compute a new guide tree .TP \fB-sample \fR sample traceback path; if not given, Viterbi is chosen .TP \fB-delta= or \-delta=estimate \fR if not given, default is used .TP \fB-epsilon= or \-epsilon=estimate \fR if not given, default is used .TP \fB-gapfreq= \fR if not given, default is used .TP \fB-gapprob= \fR if not given, default is used .TP \fB-bwidth= \fR if not given, default is used .TP \fB-distscale= \fR for branch lengths .TP \fB-nocorrection \fR no correction for pairwise distances on guide tree computation .TP \fB-notrailing \fR no trailing sequence corrcection .TP \fB-trailing= \fR for missing ends .TP \fB-penalize=true, or =false \fR penalize end gaps on pairwise alignments for guide tree .TP \fB-writemean \fR write mean posterior probability of sites .TP \fB-writeall \fR write posterior probability of each node .TP \fB-writeroot \fR write root node character probabilities .TP \fB-wag \fR use WAG probability table .TP \fB-dayhoff \fR use Dayhoff probability table .TP \fB-jtt \fR use JTT probability table .TP \fB-outfile=\fR .TP \fB\-outformat=pir, \-outformat=msf, \-outformat=phylip, or \-outformat=nexus \fR output format .TP \fB-quiet \fR no log debian/watch0000644000000000000000000000015212140036176010215 0ustar version=3 opts=uversionmangle=s/0/0\./ \ http://ueg.ulb.ac.be/ProAlign/download/src/proalign_(.+)\.tgz debian/proalign.manpages0000644000000000000000000000002212140477306012514 0ustar debian/proalign.1 debian/upstream0000644000000000000000000000063711761613477010774 0ustar Reference: Author: Ari Löytynoja and Michel C Milinkovitch Title: A hidden Markov model for progressive multiple alignment Journal: Bioinformatics Year: 2003 Volume: 19 Number: 12 Pages: 1505-13 DOI: 10.1093/bioinformatics/btg193 PMID: 12912831 URL: http://bioinformatics.oxfordjournals.org/content/19/12/1505 eprint: http://bioinformatics.oxfordjournals.org/content/19/12/1505.full.pdf+html debian/rules0000755000000000000000000000057212140477646010265 0ustar #!/usr/bin/make -f # DH_VERBOSE := 1 %: dh $@ override_dh_auto_build: mkdir -p build javac -d ./build *.java (cd build; jar cmvf ../debian/manifest.txt ProAlign.jar *) #(cd build; jar cmvf ../debian/manifest.txt ProAlign.jar proalign/ProAlign.class proalign/OutFile.class) get-orig-source: mkdir -p ../tarballs uscan --verbose --force-download --destdir=../tarballs debian/source/0000755000000000000000000000000012140534516010467 5ustar debian/source/format0000644000000000000000000000001412140256023011667 0ustar 3.0 (quilt)