debian/0000755000000000000000000000000011736661022007172 5ustar debian/pc-makegnuplot.1.xml0000644000000000000000000000737211110210556012776 0ustar Debian"> GNU"> GPL"> ]> &dhtitle; &dhpackage; &dhrelease; &dhdate; Chuong Do Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University.
chuongdo@cs.stanford.edu
&dhfirstname; &dhsurname; Wrote this manpage in DocBook XML for the Debian distribution.
&dhemail;
This program and its manpage are in the public domain. &dhucpackage; &dhsection; &dhpackage; Utility to plot annotation scores. &dhpackage; annotscores -refscores NOTE &dhpackage; is named makegnuplot in the original sources, but has been remamed to avoid collision with other program names. SEE ALSO pc-compare 1 , pc-project 1 ,from the probcons-extra package, and probcons 1 and probcons-RNA 1 from the probcons package. REFERENCE Please cite Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340. debian/probcons-extra.install0000644000000000000000000000010111110210556013504 0ustar pc-project usr/bin/ pc-makegnuplot usr/bin/ pc-compare usr/bin/ debian/watch0000644000000000000000000000012511110210556010205 0ustar version=3 http://probcons.stanford.edu/download.html probcons_v(\d+)_(\d+)\.tar\.gz debian/probcons.install0000644000000000000000000000005111110210556012367 0ustar probcons usr/bin/ probcons-RNA usr/bin/ debian/probcons.1.xml0000644000000000000000000002073111110210556011667 0ustar Debian"> GNU"> GPL"> ]> &dhtitle; &dhpackage; &dhrelease; &dhdate; Chuong Do Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University.
chuongdo@cs.stanford.edu
&dhfirstname; &dhsurname; Wrote this manpage in DocBook XML for the Debian distribution.
&dhemail;
This program and its manpage are in the public domain. &dhucpackage; &dhsection; &dhpackage; align multiple protein sequences and print to standard output &dhpackage; MFAFILE MFAFILE DESCRIPTION &dhpackage; is a tool for generating multiple alignments of protein sequences. Using a combination of probabilistic modeling and consistency-based alignment techniques, PROBCONS has achieved the highest accuracies of all alignment methods to date. On the BAliBASE benchmark alignment database, alignments produced by PROBCONS show statistically significant improvement over current programs, containing an average of 7% more correctly aligned columns than those of T-Coffee, 11% more correctly aligned columns than those of CLUSTAL W, and 14% more correctly aligned columns than those of DIALIGN. &dhpackage; aligns sequences provided in MFA format. This format consists of multiple sequences. Each sequence in MFA format begins with a single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than (>) symbol in the first column. OPTIONS use CLUSTALW output format instead of MFA REPS use 0 <= REPS <= 5 (default: 2) passes of consistency transformation REPS use 0 <= REPS <=1000 (default: 100) passes of iterative-refinement REPS use 0 <= REPS <= 20 (default: 0) rounds of pretraining generate all-pairs pairwise alignments use Viterbi algorithm to generate all pairs (automatically enables ) Report progress while aligning (default: off) FILENAME write annotation for multiple alignment to FILENAME FILENAME compute EM transition probabilities, store in FILENAME (default: no training) also reestimate emission probabilities (default: off) FILENAME read parameters from FILENAME (default: ) print sequences in alignment order rather than input order (default: off) SEE ALSO You can find more information in the manual of ProbCons, which is located in /usr/share/doc/probcons/manual.pdf in Debian systems. An experimental version of ProbCons compiled with parameters estimated via unsupervised training on BRAliBASE, probcons-RNA1, is also distributed in the ProbCons Debian package. pc-makegnufile 1 , pc-compare 1 , pc-project 1 , which are distributed separately in the probcons-extra package. REFERENCE Please cite Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340. debian/copyright0000644000000000000000000000463411736660277011147 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: ProbCons Source: http://probcons.stanford.edu/download.html Files: * Copyright: 2005-2009 Arun S Konagurthu The University of Melbourne. License: PD PROBCONS 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. PROBCONS 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: 2006-2011 Charles Plessy 2010-2012 Andreas Tille License: BSD Copyright (c) The Regents of the University of California. All rights reserved. . Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. 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. 3. Neither the name of the University 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 REGENTS 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 THE REGENTS OR CONTRIBUTORS 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. . On Debian systems you can find a copy of BSD license text at /usr/share/common-licenses/BSD. debian/probcons-extra.dirs0000644000000000000000000000002611110210556013005 0ustar usr/bin usr/share/doc debian/probcons.docs0000644000000000000000000000000711110210556011652 0ustar README debian/changelog0000644000000000000000000001063111736661022011045 0ustar probcons (1.12-9) unstable; urgency=low [ Charles Plessy ] * renamed debian/upstream-metadata.yaml to debian/upstream [ Andreas Tille ] * debian/upstream: Moved DOI+PMID to references * debian/control: - Standards-Version: 3.9.3 (no changes needed) - Fixed Vcs fields * debian/copyright: Uhmm, this package had no copyright file at all! * debian/README.source: deleted redundant handling advises for quilt * debian/{compat,control}: debhelper 9 -- Andreas Tille Tue, 03 Apr 2012 22:19:58 +0200 probcons (1.12-8) unstable; urgency=low * Standards-Version: 3.9.2 (no changes needed) * debian/patches/fix-gcc-4.6.patch: Fix gcc-4.6 build issue Closes: #625036 -- Andreas Tille Mon, 02 May 2011 17:18:09 +0200 probcons (1.12-7) unstable; urgency=low * Use dh for debian/rules, which will also switch off parallel building (Closes: #607729, #608710). * Switch to Debhelper 8 (debian/control, debian/compat). -- Charles Plessy Tue, 04 Jan 2011 06:57:45 +0900 probcons (1.12-6) unstable; urgency=low * Use proper C++ headers to fix gcc version 4.3 and higher issues (thanks for the patch to Matthias Klose) Closes: 607728 -- Andreas Tille Tue, 21 Dec 2010 21:53:42 +0100 probcons (1.12-5) unstable; urgency=low [ Charles Plessy ] * debian/control: Enhances: t-coffee. * Updated my email address. [ David Paleino ] * debian/control: - bumped Standards-Version to 3.8.0 + enabled parallel building in debian/rules - removed myself from Uploaders (will work from behind the scenes ;) ) - updated debhelper dependency on >= 6 (also debian/compat) [ Charles Plessy ] * Documented information in ‘debian/upstream-metadata.yaml’. * Removed mention of the bibliographic reference in ‘debian/control’. [ Andreas Tille ] * Added myself to uploaders * Make sure Dm-Uploader-Allowed is lower case Closes: #601509 * Standards-Version: 3.9.1 (no changes needed) * Debhelper >= 7 -> debian/rules: s/dh_clean -k/dh_prep/ * Source-Format 3.0 (quilt) * debian/README.source -- Andreas Tille Wed, 17 Nov 2010 13:22:35 +0100 probcons (1.12-4) unstable; urgency=low [ Charles Plessy ] * debian/control: - Moved the Homepage: field out from the package's description. - Allowed upload by Debian Maintainers. - Checked the compliance with Policy 3.7.3 * debian/patches: - swiched to quilt - added a fix to build with GCC 4.3 (Closes: #455625) * debian/rules: - modify Main-RNA.cc so that it uses Defaults-RNA.h (Closes: #458926) * debian/copyright: - converted to machine-readable format. [ David Paleino ] * debian/probcons.1, debian/probcons-RNA.1, debian/pc-compare.1, debian/pc-makegnuplot.1, debian/pc-project.1 added - these have been statically built. * debian/control: - B-D updated - added myself to Uploaders * debian/rules: - manpages statically built - minor changes -- Charles Plessy Fri, 04 Jan 2008 16:53:23 +0100 probcons (1.12-3) unstable; urgency=low * Fixed typos which caused incomplete cleaning (Closes: #424301). * Fixed double-building of binaries and manpages. -- Charles Plessy Wed, 16 May 2007 09:35:25 +0900 probcons (1.12-2) unstable; urgency=low * Corrected an error in the build rules making probcons-RNA, which prevented it to benefit from the fixes on probcons. (Closes: #417482) (again!) -- Charles Plessy Wed, 18 Apr 2007 22:34:51 +0900 probcons (1.12-1) unstable; urgency=low * New upstream release, buildable with gcc 4.3 (Closes: #417482) * Add Subversion repository URL to debian/control. * Including /usr/share/dpatch/dpatch.make in debian/rules. * Updated manpages using the template of docbook-xsl 1.71.0.dfsg.1-1.1. -- Charles Plessy Wed, 4 Apr 2007 09:56:46 +0900 probcons (1.11-1) unstable; urgency=low * New upstream release fixing a bug with conflict between --annot and -a options. * Mended the watch file in the source package. -- Charles Plessy Wed, 14 Feb 2007 23:15:36 +0900 probcons (1.10-1) unstable; urgency=low * Initial release Closes: #365499 -- Charles Plessy Wed, 3 May 2006 09:20:57 +0900 debian/README.Debian0000644000000000000000000000135611110210556011224 0ustar probcons for Debian ------------------- * The "compare", "project" and "makegnuplot" programs are located in the probcons-extra package and renamed "pc-compare", "pc-project" and "pc-makegnuplot" to avoid collision with other program names. * This package contains an additionnal binary which is not in the original distribution of ProbCons: probcons-RNA. It is an experimental version of ProbCons compiled with parameters estimated via unsupervised training on BRAliBASE. The parameters were downloaded from a separate archive: http://probcons.stanford.edu/probconsRNA.tar.gz, and the current version of probcons was used to build probcons-RNA. -- Charles Plessy , Wed, 18 Apr 2007 22:30:52 +0900 debian/pc-compare.1.xml0000644000000000000000000001032011110210556012061 0ustar Debian"> GNU"> GPL"> ]> &dhtitle; &dhpackage; &dhrelease; &dhdate; Chuong Do Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University.
chuongdo@cs.stanford.edu
&dhfirstname; &dhsurname; Wrote this manpage in DocBook XML for the Debian distribution.
&dhemail;
This program and its manpage are in the public domain. &dhucpackage; &dhsection; &dhpackage; Program for scoring alignments according to a reference alignment with respect to sum-of-pairs and column scores. &dhpackage; TEST_ALIGNMENT REFERENCE_ALIGNMENT BALIBASE_ANNOT_FILE NOTE &dhpackage; is named compare in the original sources, but has been remamed to avoid collision with other program names. SEE ALSO pc-makegnufile 1 , pc-project 1 ,from the probcons-extra package, and probcons 1 and probcons-RNA 1 from the probcons package. REFERENCE Please cite Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340. debian/probcons-RNA.10000644000000000000000000000305611110210556011507 0ustar .\" Title: PROBCONS-RNA .\" Author: Chuong Do .\" Generator: DocBook XSL Stylesheets v1.73.2 .\" Date: 2007-04-04 .\" Manual: Probcons Manual .\" Source: probcons-RNA 1.12 .\" .TH "PROBCONS\-RNA" "1" "2007\-04\-04" "probcons-RNA 1.12" "Probcons Manual" .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .SH "NAME" probcons-RNA - An experimental version of ProbCons compiled with parameters estimated via unsupervised training on BRAliBASE. .SH "DESCRIPTION" .PP See the manpage of \fBprobcons\fR(1) for the command\-line arguments, and \fI/usr/share/doc/README\.Debian\fR for more informations about how probcons\-RNA has been built\. .SH "SEE ALSO" .sp .RS 4 \h'-04'\(bu\h'+03'You can find more information in the manual of ProbCons, which is located in \fI/usr/share/doc/probcons/manual\.pdf\fR in Debian systems\. .RE .sp .RS 4 \h'-04'\(bu\h'+03' \fBprobcons\fR(1), \fBpc-makegnufile\fR(1), \fBpc-compare\fR(1), \fBpc-project\fR(1), which are distributed separately in the probcons\-extra package\. .RE .SH "AUTHORS" .PP \fBChuong Do\fR <\&chuongdo@cs\.stanford\.edu\&> .sp -1n .IP "" 4 Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University\. .PP \fBCharles Plessy\fR <\&charles\-debian\-nospam@plessy\.org\&> .sp -1n .IP "" 4 Wrote this manpage in DocBook XML for the Debian distribution\. .SH "COPYRIGHT" .PP This program and its manpage are in the public domain\. .sp debian/pc-compare.10000644000000000000000000000331311110210556011266 0ustar .\" Title: PC-COMPARE .\" Author: Chuong Do .\" Generator: DocBook XSL Stylesheets v1.73.2 .\" Date: 2007-04-04 .\" Manual: Probcons Manual .\" Source: pc-compare 1.12 .\" .TH "PC\-COMPARE" "1" "2007\-04\-04" "pc-compare 1.12" "Probcons Manual" .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .SH "NAME" pc-compare - Program for scoring alignments according to a reference alignment with respect to sum-of-pairs and column scores. .SH "SYNOPSIS" .HP 11 \fBpc\-compare\fR [\fITEST_ALIGNMENT\fR] [\fIREFERENCE_ALIGNMENT\fR] [\fIBALIBASE_ANNOT_FILE\fR] [\fB\-col\fR] [\fB\-core\fR] [\fB\-caps\fR] [\fB\-annot\ \fR\fB\fIFILENAME\fR\fR] .SH "NOTE" .PP pc\-compare is named \fIcompare\fR in the original sources, but has been remamed to avoid collision with other program names\. .SH "SEE ALSO" .PP \fBpc-makegnufile\fR(1), \fBpc-project\fR(1),from the probcons\-extra package, and \fBprobcons\fR(1) and \fBprobcons-RNA\fR(1) from the probcons package\. .SH "REFERENCE" .PP Please cite Do, C\.B\., Mahabhashyam, M\.S\.P\., Brudno, M\., and Batzoglou, S\. 2005\. PROBCONS: Probabilistic Consistency\-based Multiple Sequence Alignment\. Genome Research 15: 330\-340\. .SH "AUTHORS" .PP \fBChuong Do\fR <\&chuongdo@cs\.stanford\.edu\&> .sp -1n .IP "" 4 Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University\. .PP \fBCharles Plessy\fR <\&charles\-debian\-nospam@plessy\.org\&> .sp -1n .IP "" 4 Wrote this manpage in DocBook XML for the Debian distribution\. .SH "COPYRIGHT" .PP This program and its manpage are in the public domain\. .sp debian/Defaults-RNA.h0000644000000000000000000000340611110210556011517 0ustar ///////////////////////////////////////////////////////////////// // Defaults.h // // Default constants for use in PROBCONS. The emission // probabilities were computed using the program used to build // the BLOSUM62 matrix from the BLOCKS 5.0 dataset. Transition // parameters were obtained via unsupervised EM training on the // BALIBASE 2.0 benchmark alignment database. ///////////////////////////////////////////////////////////////// #ifndef DEFAULTS_H #define DEFAULTS_H #include using namespace std; float initDistrib1Default[] = { 0.9588437676f, 0.0205782652f, 0.0205782652f }; float gapOpen1Default[] = { 0.0190259293f, 0.0190259293f }; float gapExtend1Default[] = { 0.3269913495f, 0.3269913495f }; float initDistrib2Default[] = { 0.9615409374f, 0.0000004538f, 0.0000004538f, 0.0192291681f, 0.0192291681f }; float gapOpen2Default[] = { 0.0082473317f, 0.0082473317f, 0.0107844425f, 0.0107844425f }; float gapExtend2Default[] = { 0.3210460842f, 0.3210460842f, 0.3298229277f, 0.3298229277f }; string alphabetDefault = "ACGUTN"; float emitSingleDefault[6] = { 0.2270790040f, 0.2422080040f, 0.2839320004f, 0.2464679927f, 0.2464679927f, 0.0003124650f }; float emitPairsDefault[6][6] = { { 0.1487240046f, 0.0184142999f, 0.0361397006f, 0.0238473993f, 0.0238473993f, 0.0000375308f }, { 0.0184142999f, 0.1583919972f, 0.0275536999f, 0.0389291011f, 0.0389291011f, 0.0000815823f }, { 0.0361397006f, 0.0275536999f, 0.1979320049f, 0.0244289003f, 0.0244289003f, 0.0000824765f }, { 0.0238473993f, 0.0389291011f, 0.0244289003f, 0.1557479948f, 0.1557479948f, 0.0000743985f }, { 0.0238473993f, 0.0389291011f, 0.0244289003f, 0.1557479948f, 0.1557479948f, 0.0000743985f }, { 0.0000375308f, 0.0000815823f, 0.0000824765f, 0.0000743985f, 0.0000743985f, 0.0000263252f } }; #endif debian/pc-project.10000644000000000000000000000303311110210556011305 0ustar .\" Title: PC-PROJECT .\" Author: Chuong Do .\" Generator: DocBook XSL Stylesheets v1.73.2 .\" Date: 2007-04-04 .\" Manual: Probcons Manual .\" Source: pc-project 1.12 .\" .TH "PC\-PROJECT" "1" "2007\-04\-04" "pc-project 1.12" "Probcons Manual" .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .SH "NAME" pc-project - Program to project multiple alignment to pairwise alignments. .SH "SYNOPSIS" .HP 11 \fBpc\-project\fR [\fIALIGNMENT\fR] [\-nocompressgaps] .SH "NOTE" .PP pc\-project is named \fIproject\fR in the original sources, but has been remamed to avoid collision with other program names\. .SH "SEE ALSO" .PP \fBpc-makegnufile\fR(1), \fBpc-compare\fR(1),from the probcons\-extra package, and \fBprobcons\fR(1) and \fBprobcons-RNA\fR(1) from the probcons package\. .SH "REFERENCE" .PP Please cite Do, C\.B\., Mahabhashyam, M\.S\.P\., Brudno, M\., and Batzoglou, S\. 2005\. PROBCONS: Probabilistic Consistency\-based Multiple Sequence Alignment\. Genome Research 15: 330\-340\. .SH "AUTHORS" .PP \fBChuong Do\fR <\&chuongdo@cs\.stanford\.edu\&> .sp -1n .IP "" 4 Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University\. .PP \fBCharles Plessy\fR <\&charles\-debian\-nospam@plessy\.org\&> .sp -1n .IP "" 4 Wrote this manpage in DocBook XML for the Debian distribution\. .SH "COPYRIGHT" .PP This program and its manpage are in the public domain\. .sp debian/source/0000755000000000000000000000000011557545243010501 5ustar debian/source/format0000644000000000000000000000001311452534644011703 0ustar 3.0 (quilt)debian/compat0000644000000000000000000000000211736660764010404 0ustar 9 debian/patches/0000755000000000000000000000000011736657375010641 5ustar debian/patches/fix-gcc-4.6.patch0000644000000000000000000000033411557545433013477 0ustar --- probcons.orig/SafeVector.h +++ probcons/SafeVector.h @@ -10,6 +10,7 @@ #include #include +#include ///////////////////////////////////////////////////////////////// // SafeVector debian/patches/fix-gcc-4.5-headers0000644000000000000000000000223611504215221013771 0ustar Author: Matthias Klose Description: Fix compile issues with gcc version 4.3 and higher Origin: http://bugs.debian.org/607728 Forwarded: yes --- probcons.orig/ProbabilisticModel.h +++ probcons/ProbabilisticModel.h @@ -12,6 +12,7 @@ #include #include #include +#include #include "SafeVector.h" #include "ScoreType.h" #include "SparseMatrix.h" --- probcons.orig/ProjectPairwise.cc +++ probcons/ProjectPairwise.cc @@ -16,6 +16,7 @@ #include #include #include +#include #include #include --- probcons.orig/CompareToRef.cc +++ probcons/CompareToRef.cc @@ -16,6 +16,7 @@ #include #include #include +#include #include #include --- probcons.orig/FixRef.cc +++ probcons/FixRef.cc @@ -17,6 +17,7 @@ #include #include #include +#include #include #include --- probcons.orig/Main.cc +++ probcons/Main.cc @@ -21,6 +21,7 @@ #include #include #include +#include #include #include debian/patches/series0000644000000000000000000000015011736657010012034 0ustar 10_add-RNA-in-Makefile.patch 11-Rename-programs-in-Makefile.patch fix-gcc-4.5-headers fix-gcc-4.6.patch debian/patches/11-Rename-programs-in-Makefile.patch0000644000000000000000000000341311736657375017260 0ustar The purpose of this patch is to rename programs with a too generic name, to avoid conflicts on file names. --- probcons.orig/Makefile +++ probcons/Makefile @@ -35,7 +35,7 @@ # 3) Dependencies ################################################################################ -TARGETS = probcons probcons-RNA compare project makegnuplot +TARGETS = probcons probcons-RNA pc-compare pc-project pc-makegnuplot .PHONY : all all : $(TARGETS) @@ -43,8 +43,8 @@ probcons : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h Main.cc $(CXX) $(CXXFLAGS) -lm -o probcons Main.cc -compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc - $(CXX) $(CXXFLAGS) -o compare CompareToRef.cc +pc-compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc + $(CXX) $(CXXFLAGS) -o pc-compare CompareToRef.cc probcons-RNA : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults-RNA.h SafeVector.h Main-RNA.cc $(CXX) $(CXXFLAGS-RNA) -lm -o probcons-RNA Main-RNA.cc @@ -52,11 +52,11 @@ fixref : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h FixRef.cc $(CXX) $(CXXFLAGS) -o fixref FixRef.cc -project : MultiSequence.h Sequence.h SafeVector.h ProjectPairwise.cc - $(CXX) $(CXXFLAGS) -o project ProjectPairwise.cc +pc-project : MultiSequence.h Sequence.h SafeVector.h ProjectPairwise.cc + $(CXX) $(CXXFLAGS) -o pc-project ProjectPairwise.cc -makegnuplot : MakeGnuPlot.cc - $(CXX) $(CXXFLAGS) -o makegnuplot MakeGnuPlot.cc +pc-makegnuplot : MakeGnuPlot.cc + $(CXX) $(CXXFLAGS) -o pc-makegnuplot MakeGnuPlot.cc .PHONY : clean clean: debian/patches/10_add-RNA-in-Makefile.patch0000644000000000000000000000322211736657367015447 0ustar The purpose of this patch is to add a rule for the building of probcons-RNA. --- probcons.orig/Makefile +++ probcons/Makefile @@ -16,6 +16,7 @@ ################################################################################ OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.12" +OTHERFLAGS-RNA = -DNumInsertStates=1 -DVERSION="1.12" # debug mode #CXXFLAGS = -g -W -Wall -pedantic -DENABLE_CHECKS -fno-inline $(OTHERFLAGS) @@ -25,13 +26,16 @@ # release mode #CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer + CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops +CXXFLAGS-RNA = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS-RNA) -funroll-loops + ################################################################################ # 3) Dependencies ################################################################################ -TARGETS = probcons compare project makegnuplot +TARGETS = probcons probcons-RNA compare project makegnuplot .PHONY : all all : $(TARGETS) @@ -42,6 +46,9 @@ compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc $(CXX) $(CXXFLAGS) -o compare CompareToRef.cc +probcons-RNA : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults-RNA.h SafeVector.h Main-RNA.cc + $(CXX) $(CXXFLAGS-RNA) -lm -o probcons-RNA Main-RNA.cc + fixref : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h FixRef.cc $(CXX) $(CXXFLAGS) -o fixref FixRef.cc debian/probcons.manpages0000644000000000000000000000005011110210556012513 0ustar debian/probcons.1 debian/probcons-RNA.1 debian/probcons.copyright0000644000000000000000000000174311110210556012742 0ustar ProbCons was downloaded from http://probcons.stanford.edu/probcons_v1_10.tar.gz The modified files for RNA alignment were downloaded from http://probcons.stanford.edu/probconsRNA.tar.gz Files: debian/* Copyright: © 2006-2008 Charles Plessy © 2007 David Paleino Licence: PD Please treat this work as if it were in the public domain. Files: * Licence: PD ProbCons was written by by Chuong Do in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University. . PROBCONS 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. PROBCONS is distributed WITHOUT WARRANTY, express or implied. The authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for loss due to reliance on the program. debian/pc-makegnuplot.10000644000000000000000000000303111110210556012163 0ustar .\" Title: PC-MAKEGNUPLOT .\" Author: Chuong Do .\" Generator: DocBook XSL Stylesheets v1.73.2 .\" Date: 2007-04-04 .\" Manual: Probcons Manual .\" Source: pc-makegnuplot 1.12 .\" .TH "PC\-MAKEGNUPLOT" "1" "2007\-04\-04" "pc-makegnuplot 1.12" "Probcons Manual" .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .SH "NAME" pc-makegnuplot - Utility to plot annotation scores. .SH "SYNOPSIS" .HP 15 \fBpc\-makegnuplot\fR [\fIannotscores\fR] [\-refscores] .SH "NOTE" .PP pc\-makegnuplot is named \fImakegnuplot\fR in the original sources, but has been remamed to avoid collision with other program names\. .SH "SEE ALSO" .PP \fBpc-compare\fR(1), \fBpc-project\fR(1),from the probcons\-extra package, and \fBprobcons\fR(1) and \fBprobcons-RNA\fR(1) from the probcons package\. .SH "REFERENCE" .PP Please cite Do, C\.B\., Mahabhashyam, M\.S\.P\., Brudno, M\., and Batzoglou, S\. 2005\. PROBCONS: Probabilistic Consistency\-based Multiple Sequence Alignment\. Genome Research 15: 330\-340\. .SH "AUTHORS" .PP \fBChuong Do\fR <\&chuongdo@cs\.stanford\.edu\&> .sp -1n .IP "" 4 Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University\. .PP \fBCharles Plessy\fR <\&charles\-debian\-nospam@plessy\.org\&> .sp -1n .IP "" 4 Wrote this manpage in DocBook XML for the Debian distribution\. .SH "COPYRIGHT" .PP This program and its manpage are in the public domain\. .sp debian/rules0000755000000000000000000000167311507371101010251 0ustar #!/usr/bin/make -f %: dh $@ BINARIES = probcons probcons-RNA pc-project pc-compare pc-makegnuplot override_dh_auto_build: cp Main.cc Main-RNA.cc sed -i s/Defaults.h/Defaults-RNA.h/ Main-RNA.cc cp debian/Defaults-RNA.h Defaults-RNA.h dh_auto_build override_dh_link: rm -rf $(CURDIR)/debian/probcons-extra/usr/share/doc/probcons-extra dh_link -p probcons-extra usr/share/doc/probcons usr/share/doc/probcons-extra override_dh_clean: dh_clean $(BINARIES) Main-RNA.cc Defaults-RNA.h XP = xsltproc \ -''-nonet \ -''-param man.charmap.use.subset "0" \ -''-param make.year.ranges "1" \ -''-param make.single.year.ranges "1" \ -o debian/ manpages: debian/probcons.1.xml debian/probcons-RNA.1.xml debian/pc-project.1.xml debian/pc-compare.1.xml debian/pc-makegnuplot.1.xml $(XP) debian/probcons.1.xml $(XP) debian/probcons-RNA.1.xml $(XP) debian/pc-project.1.xml $(XP) debian/pc-compare.1.xml $(XP) debian/pc-makegnuplot.1.xml debian/probcons.10000644000000000000000000001000211110210556011056 0ustar .\" Title: PROBCONS .\" Author: Chuong Do .\" Generator: DocBook XSL Stylesheets v1.73.2 .\" Date: 2007-04-04 .\" Manual: Probcons Manual .\" Source: probcons 1.12 .\" .TH "PROBCONS" "1" "2007\-04\-04" "probcons 1.12" "Probcons Manual" .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .SH "NAME" probcons - align multiple protein sequences and print to standard output .SH "SYNOPSIS" .HP 9 \fBprobcons\fR [\fB\fIOPTION\fR\fR] [\fIMFAFILE\fR] [\fIMFAFILE\fR] .SH "DESCRIPTION" .PP \fBprobcons\fR is a tool for generating multiple alignments of protein sequences\. Using a combination of probabilistic modeling and consistency\-based alignment techniques, PROBCONS has achieved the highest accuracies of all alignment methods to date\. On the BAliBASE benchmark alignment database, alignments produced by PROBCONS show statistically significant improvement over current programs, containing an average of 7% more correctly aligned columns than those of T\-Coffee, 11% more correctly aligned columns than those of CLUSTAL W, and 14% more correctly aligned columns than those of DIALIGN\. .PP \fBprobcons\fR aligns sequences provided in MFA format\. This format consists of multiple sequences\. Each sequence in MFA format begins with a single\-line description, followed by lines of sequence data\. The description line is distinguished from the sequence data by a greater\-than (\(lq>\(rq) symbol in the first column\. .SH "OPTIONS" .PP \fB\-clustalw\fR .RS 4 use CLUSTALW output format instead of MFA .RE .PP \fB\-c\fR \fB\-\-consistency\fR \fIREPS\fR .RS 4 use 0 <= \fIREPS\fR <= 5 (default: 2) passes of consistency transformation .RE .PP \fB\-ir\fR \fB\-\-iterative\-refinement\fR \fIREPS\fR .RS 4 use 0 <= \fIREPS\fR <=1000 (default: 100) passes of iterative\-refinement .RE .PP \fB\-pre\fR \fB\-\-pre\-training\fR \fIREPS\fR .RS 4 use 0 <= \fIREPS\fR <= 20 (default: 0) rounds of pretraining .RE .PP \fB\-pairs\fR .RS 4 generate all\-pairs pairwise alignments .RE .PP \fB\-viterbi\fR .RS 4 use Viterbi algorithm to generate all pairs (automatically enables \fB\-pairs\fR) .RE .PP \fB\-v\fR \fB\-\-verbose\fR .RS 4 Report progress while aligning (default: off) .RE .PP \fB\-annot\fR \fIFILENAME\fR .RS 4 write annotation for multiple alignment to \fIFILENAME\fR .RE .PP \fB\-t\fR \fB\-\-train\fR \fIFILENAME\fR .RS 4 compute EM transition probabilities, store in \fIFILENAME\fR (default: no training) .RE .PP \fB\-e\fR \fB\-\-emissions\fR .RS 4 also reestimate emission probabilities (default: off) .RE .PP \fB\-p\fR \fB\-\-paramfile\fR \fIFILENAME\fR .RS 4 read parameters from \fIFILENAME\fR (default: ) .RE .PP \fB\-a\fR \fB\-\-alignment\-order\fR .RS 4 print sequences in alignment order rather than input order (default: off) .RE .SH "SEE ALSO" .sp .RS 4 \h'-04'\(bu\h'+03'You can find more information in the manual of ProbCons, which is located in \fI/usr/share/doc/probcons/manual\.pdf\fR in Debian systems\. .RE .sp .RS 4 \h'-04'\(bu\h'+03'An experimental version of ProbCons compiled with parameters estimated via unsupervised training on BRAliBASE, \fBprobcons-RNA\fR(1), is also distributed in the ProbCons Debian package\. .RE .sp .RS 4 \h'-04'\(bu\h'+03' \fBpc-makegnufile\fR(1), \fBpc-compare\fR(1), \fBpc-project\fR(1), which are distributed separately in the probcons\-extra package\. .RE .SH "REFERENCE" .PP Please cite Do, C\.B\., Mahabhashyam, M\.S\.P\., Brudno, M\., and Batzoglou, S\. 2005\. PROBCONS: Probabilistic Consistency\-based Multiple Sequence Alignment\. Genome Research 15: 330\-340\. .SH "AUTHORS" .PP \fBChuong Do\fR <\&chuongdo@cs\.stanford\.edu\&> .sp -1n .IP "" 4 Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University\. .PP \fBCharles Plessy\fR <\&charles\-debian\-nospam@plessy\.org\&> .sp -1n .IP "" 4 Wrote this manpage in DocBook XML for the Debian distribution\. .SH "COPYRIGHT" .PP This program and its manpage are in the public domain\. .sp debian/probcons-extra.manpages0000644000000000000000000000010011110210556013630 0ustar debian/pc-makegnuplot.1 debian/pc-compare.1 debian/pc-project.1 debian/control0000644000000000000000000000356311736660770010615 0ustar Source: probcons 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/probcons/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/probcons/trunk/ Homepage: http://probcons.stanford.edu/ Package: probcons Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: probcons-extra Enhances: t-coffee Description: PROBabilistic CONSistency-based multiple sequence alignment Tool for generating multiple alignments of protein sequences. Using a combination of probabilistic modeling and consistency-based alignment techniques, PROBCONS has achieved the highest accuracies of all alignment methods to date. On the BAliBASE benchmark alignment database, alignments produced by PROBCONS show statistically significant improvement over current programs, containing an average of 7% more correctly aligned columns than those of T-Coffee, 11% more correctly aligned columns than those of CLUSTAL W, and 14% more correctly aligned columns than those of DIALIGN. Package: probcons-extra Architecture: any Depends: probcons (= ${binary:Version}), ${shlibs:Depends}, ${misc:Depends} Suggests: gnuplot-nox | gnuplot-x11 Priority: extra Description: Extra programs from the probcons package Contains the convert, project and makgnuplot programs from the probcons package, which have been renamed to pc-compare, pc-project and pc-makegnuplot respectively to avoid collisions with other program names. These programs are mostly useful for testing purposes and are not required for the normal usage of Probcons. . Probcons is a tool for generating multiple alignments of protein sequences. debian/probcons-RNA.1.xml0000644000000000000000000000747411110210556012316 0ustar Debian"> GNU"> GPL"> ]> &dhtitle; &dhproduct; &dhrelease; &dhdate; Chuong Do Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University.
chuongdo@cs.stanford.edu
&dhfirstname; &dhsurname; Wrote this manpage in DocBook XML for the Debian distribution.
&dhemail;
This program and its manpage are in the public domain. PROBCONS-RNA &dhsection; &dhproduct; An experimental version of ProbCons compiled with parameters estimated via unsupervised training on BRAliBASE. DESCRIPTION See the manpage of probcons1 for the command-line arguments, and /usr/share/doc/README.Debian for more informations about how probcons-RNA has been built. SEE ALSO You can find more information in the manual of ProbCons, which is located in /usr/share/doc/probcons/manual.pdf in Debian systems. probcons 1 , pc-makegnufile 1 , pc-compare 1 , pc-project 1 , which are distributed separately in the probcons-extra package. debian/upstream0000644000000000000000000000114211736655675010774 0ustar Contact: Chuong Do Homepage: http://probcons.stanford.edu/ Name: ProbCons Reference: author: Do, Chuong B. and Mahabhashyam, Mahathi S.P. and Brudno, Michael and Batzoglou, Serafim title: > ProbCons: Probabilistic consistency-based multiple sequence alignment journal: Genome Research volume: 15 number: 2 pages: 330-340 year: 2005 DOI: 10.1101/gr.2821705 PMID: 15687296 URL: http://genome.cshlp.org/content/15/2/330.abstract eprint: http://genome.cshlp.org/content/15/2/330.full.pdf+html Watch: http://probcons.stanford.edu/download.html probcons_v(\d+)_(\d+)\.tar\.gz debian/pc-project.1.xml0000644000000000000000000000742411110210556012114 0ustar Debian"> GNU"> GPL"> ]> &dhtitle; &dhpackage; &dhrelease; &dhdate; Chuong Do Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University.
chuongdo@cs.stanford.edu
&dhfirstname; &dhsurname; Wrote this manpage in DocBook XML for the Debian distribution.
&dhemail;
This program and its manpage are in the public domain. &dhucpackage; &dhsection; &dhpackage; Program to project multiple alignment to pairwise alignments. &dhpackage; ALIGNMENT -nocompressgaps NOTE &dhpackage; is named project in the original sources, but has been remamed to avoid collision with other program names. SEE ALSO pc-makegnufile 1 , pc-compare 1 ,from the probcons-extra package, and probcons 1 and probcons-RNA 1 from the probcons package. REFERENCE Please cite Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340. debian/probcons.dirs0000644000000000000000000000005511110210556011666 0ustar usr/bin usr/share/doc usr/share/doc/probcons