debian/0000755000000000000000000000000012241170734007167 5ustar debian/control0000644000000000000000000000244312241167621010576 0ustar Source: probalign Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Section: science Priority: optional Build-Depends: debhelper (>= 9), help2man Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/probalign/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/probalign/trunk/ Homepage: http://cs.njit.edu/usman/probalign/ Package: probalign Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: multiple sequence alignment using partition function posterior probabilities Probalign uses partition function posterior probability estimates to compute maximum expected accuracy multiple sequence alignments. It performs statistically significantly better than the leading alignment programs Probcons v1.1, MAFFT v5.851, and MUSCLE v3.6 on BAliBASE 3.0, HOMSTRAD, and OXBENCH benchmarks. Probalign improvements are largest on datasets containing N/C terminal extensions and on datasets with long and heterogeneous length sequences. On heteregeneous length datasets containing repeats Probalign alignment accuracy is 10% and 15% higher than the other three methods when standard deviation of length is at least 300 and 400. debian/install0000644000000000000000000000002211522270274010553 0ustar probalign usr/bin debian/rules0000755000000000000000000000122312241167544010252 0ustar #!/usr/bin/make -f # debian/rules for probalign # Andreas Tille # LGPL-3 # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 VERSION := $(shell dpkg-parsechangelog | sed -ne 's/^Version: \(\([0-9]\+\):\)\?\(.*\)-.*/\3/p') PKG := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p') %: dh $@ override_dh_auto_install: help2man --name="Align sequences in MFAFILE(s) and print result to standard output" \ --no-discard-stderr \ --version-string=$(VERSION) \ --help-option=" " \ --no-info \ $(CURDIR)/probalign > $(CURDIR)/debian/$(PKG)/usr/share/man/man1/probalign.1 debian/watch0000644000000000000000000000010511522263454010217 0ustar version=3 http://cs.njit.edu/usman/probalign/probalign([\d\.]+)\.tgz debian/upstream0000644000000000000000000000106012214301123010733 0ustar Contact: Usman Roshan Homepage: http://cs.njit.edu/usman/probalign/ Name: Probalign Reference: AUTHOR: Usman Roshan and Dennis R. Livesay TITLE: > Probalign: multiple sequence alignment using partition function posterior probabilities JOURNAL: Bioinformatics YEAR: 2006 PAGES: 2715-21 VOLUME: 22 NUMBER: 22 URL: http://bioinformatics.oxfordjournals.org/content/22/22/2715.short eprint: http://bioinformatics.oxfordjournals.org/content/22/22/2715.full.pdf+html ISSN: 1460-2059 DOI: 10.1093/bioinformatics/btl472 PMID: 16954142 debian/copyright0000644000000000000000000000172712241167776011145 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: Probalign Upstream-Contact: Usman Roshan Source: http://cs.njit.edu/usman/probalign/ Files: * Copyright: © 2010 Satish Chikkagoudar and Usman Roshan © 2005 Chuong Dousing (PROBCONS 1.1) © 2002 Ulrike Muckstein (probA) License: PD PROBALIGN has been made freely available as PUBLIC DOMAIN software and hence is not subject to copyright in the United States. This system and/or any portion of the source code may be used, modified, or redistributed without restrictions... PROBALIGN is distributed WITHOUT WARRANTY, express or implied. The authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for loss due to reliance on the program. Files: debian/* Copyright: © 2011-2013 Andreas Tille License: LGPL-3 On Debian GNU/Linux systems the full text of LGPL-3 license can be found at /usr/share/common-licenses/LGPL-3 debian/source/0000755000000000000000000000000011520762120010462 5ustar debian/source/format0000644000000000000000000000001411473514012011672 0ustar 3.0 (quilt) debian/changelog0000644000000000000000000000177612241170734011054 0ustar probalign (1.4-3) unstable; urgency=low [ Andreas Tille ] * debian/upstream - fix typo (s/TITILE/TITLE/) - moved DOI+PMID to references - separate authors by ' and ' - added eprint * debian/control: - cme fix dpkg-control - debhelper 9 - removed quilt Build-Depends - canonical Vcs URLs * debian/copyright: DEP5 * debian/patches/hardening.patch: Propagate hardening options [ Charles Plessy ] * Add missing word in long description (Closes: #703253). -- Andreas Tille Thu, 14 Nov 2013 16:41:20 +0100 probalign (1.4-2) unstable; urgency=low * Standards-Version: 3.9.2 (no changes needed) * Debhelper 8 (control+compat) * debian/patches/fix-gcc-4.6.patch Closes: #624979 -- Andreas Tille Mon, 02 May 2011 17:02:21 +0200 probalign (1.4-1) unstable; urgency=low * Initial release (Closes: #611828) (reupload with LGPL-3 license for debian/*) -- Andreas Tille Wed, 02 Feb 2011 15:45:54 +0100 debian/patches/0000755000000000000000000000000012241170721010612 5ustar debian/patches/gcc_fixes.patch0000644000000000000000000000051611522267104013572 0ustar Author: Andreas Tille Date: Wed, 02 Feb 2011 15:45:54 +0100 Description: Patches to compile with gcc-4.4 --- probalign1.4.orig/Main.cc +++ probalign1.4/Main.cc @@ -15,6 +15,8 @@ #include #include #include +#include +#include //struct for column reliability debian/patches/fix-gcc-4.6.patch0000644000000000000000000000064512241170514013465 0ustar Author: Andreas Tille LastChanged: Mon, 02 May 2011 17:02:21 +0200 BugsDebian: http://bugs.debian.org/624979 Description: Add missing include that is required since gcc-4.6 --- probalign1.4.orig/SafeVector.h +++ probalign1.4/SafeVector.h @@ -10,6 +10,7 @@ #include #include +#include ///////////////////////////////////////////////////////////////// // SafeVector debian/patches/hardening.patch0000644000000000000000000000130612241170721013572 0ustar Author: Andreas Tille LastChanged: Thu, 14 Nov 2013 16:41:20 +0100 Description: Propagate hardening options --- a/Makefile +++ b/Makefile @@ -1,11 +1,11 @@ CXX = g++ -CXXFLAGS = -O3 -W -Wall -funroll-loops +CXXFLAGS += -O3 -W -Wall -funroll-loops TARGET = probalign all : $(TARGET) probalign : MultiSequence.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h SafeVector.h Main.cc Sequence.h PostProbs.cc ComputeAlignment.cc ReadMatrix.cc Matrix.h - $(CXX) $(CXXFLAGS) -lm -o $(TARGET) Main.cc PostProbs.cc ComputeAlignment.cc ReadMatrix.cc + $(CXX) $(CXXFLAGS) -lm -o $(TARGET) Main.cc PostProbs.cc ComputeAlignment.cc ReadMatrix.cc $(LDFLAGS) clean: rm -f $(TARGET) debian/patches/series0000644000000000000000000000006212241170573012032 0ustar gcc_fixes.patch fix-gcc-4.6.patch hardening.patch debian/compat0000644000000000000000000000000212241167533010370 0ustar 9 debian/dirs0000644000000000000000000000002311522270602010042 0ustar usr/share/man/man1 debian/docs0000644000000000000000000000000711522302005010024 0ustar README