New upstream version 12.00.7fb08c2 (c1276b4a) · Commits · Debian Med / t-coffee

example/proteases_large.fasta

0 → 100644

+476 −0

File added.

Preview size limit exceeded, changes collapsed.

install

+105 −67

Original line number	Diff line number	Diff line
		@@ -55,7 +55,7 @@ our $FFLAGS="";

		my $install="all";
		my $default_update_action="no_update";
		########################################################
		###########################################################
		my @required_applications=("wget_OR_curl");
		########### Mode Definitions ##############################
		#
		@@ -128,7 +128,8 @@ our ($ROOT_INSTALL, $NO_QUESTION, $default_update_action,$BINARIES_ONLY,$force,
		if ( ($cl=~/-root/)){$ROOT_INSTALL=1;}
		if ( ($cl=~/-no_question/)){$NO_QUESTION=1;}
		if ( ($cl=~/-update/)){$default_update_action="update";}
		if ( ($cl=~/-binaries/)){$BINARIES_ONLY=1;}
		$BINARIES_ONLY=1;
		if ( ($cl=~/-nobinaries/)){$BINARIES_ONLY=0;}
		if ( ($cl=~/-force/)){$force=1;$default_update_action="update"}
		if ( ($cl=~/-exec=\s*(\S+)/)){$INSTALL_DIR=$1;}
		if ( ($cl=~/-plugins=\s*(\S+)/)){$PLUGINS_DIR=$1;}
		@@ -631,7 +632,7 @@ sub install_pg
		$PG{$pg}{old}=$previous;

		if ($PG{$pg} {language2} eq "Perl"){&install_perl_package ($pg);}
		elsif ($BINARIES_ONLY && &install_binary_package ($pg)){$PG{$pg}{from_binary}=1;}
		elsif ($pg ne "t_coffee" && $BINARIES_ONLY && &install_binary_package ($pg)){$PG{$pg}{from_binary}=1;}
		elsif (&install_source_package ($pg)){;}
		else
		{
		@@ -1039,6 +1040,7 @@ sub install_source_package
		#
		elsif ( $pg eq "proda")
		{
		`sed -i '' 's/int errno = 0;/int errno; errno = 0;/' Main.cc`;
		&add_C_libraries("AlignedFragment.h", "vector", "iostream", "cstring","cstdlib");
		&add_C_libraries("Main.cc", "vector", "climits");
		&add_C_libraries("Sequence.cc", "stdlib.h", "cstdio");
		@@ -1091,6 +1093,7 @@ sub install_source_package
		elsif ( $pg eq "retree")
		{
		chdir "src";
		&flush_command ("cp Makefile.unx Makefile");
		&flush_command ("make $arguments all");
		&flush_command ("make put");
		system "cp ../exe/* $BIN";
		@@ -1168,11 +1171,7 @@ sub install_binary_package

		if (!&supported_os($OS)){return 0;}
		if ( $PG{$pg}{binary}){$name=$PG{$pg}{binary};}
		else
		{
		$name=$pg;
		if ( $OS eq "windows"){$name.=".exe";}
		}
		else {$name=$pg;}

		$download="$WEB_BASE/Packages/Binaries/$OS/$name";

		@@ -1201,23 +1200,9 @@ sub install_binary_package
		`gunzip $name`;
		`tar -xvf $pg.tar`;
		chdir $pg;
		if ( $pg eq "mafft")
		{
		if ($ROOT_INSTALL)
		{
		&root_run ("You Must be Roor to Install MAFFT\n", "$CP mafft/bin/* /usr/local/mafft;mkdir /usr/local/mafft/; $CP mafft/lib/* /usr/local/bin/");
		}
		else
		{
		`$CP $TMP/$pg/bin/* $BIN $SILENT`;
		`$CP $TMP/$pg/lib/* $BIN $SILENT`;
		}
		}
		else
		{
		if (-e "$TMP/$pg/data"){`$CP $TMP/$pg/data/* $TCM $SILENT`;}
		if (!($pg=~/\*/)){`rm -rf $pg`;}
		}
		`chmod u+x *`;
		`mv * $BIN`;
		#if (!($pg=~/\*/)){`rm -rf $pg`;}
		}
		else
		{
		@@ -1331,6 +1316,8 @@ sub repo_load
		{
		my ($pg)=(@_);

		#Bypass the Repository Cache
		return 0;
		# check that all required data are available
		if( $REPO_ROOT eq "" ) { return 0; }

		@@ -1558,7 +1545,7 @@ $PG{"t_coffee"}{"type"}="sequence_multiple_aligner";
		$PG{"t_coffee"}{"ADDRESS"}="http://www.tcoffee.org";
		$PG{"t_coffee"}{"language"}="C++";
		$PG{"t_coffee"}{"language2"}="CXX";
		$PG{"t_coffee"}{"source"}="http://www.tcoffee.org/Packages/T-COFFEE_distribution.tar.gz";
		$PG{"t_coffee"}{"source"}="http://www.tcoffee.org/Packages/Stable/Latest/T-COFFEE_distribution.tar.gz";
		$PG{"t_coffee"}{"update_action"}="always";
		$PG{"t_coffee"}{"mode"}="tcoffee,mcoffee,rcoffee,expresso,3dcoffee";
		$PG{"clustalo"}{"4_TCOFFEE"}="CLUSTALO";
		@@ -1566,9 +1553,10 @@ $PG{"clustalo"}{"type"}="sequence_multiple_aligner";
		$PG{"clustalo"}{"ADDRESS"}="http://www.clustal.org/omega/";
		$PG{"clustalo"}{"language"}="C++";
		$PG{"clustalo"}{"language2"}="C++";
		$PG{"clustalo"}{"source"}="http://www.clustal.org/omega/clustal-omega-1.1.0.tar.gz";
		$PG{"clustalo"}{"source"}="http://www.clustal.org/omega/clustal-omega-1.2.4.tar.gz";
		$PG{"clustalo"}{"mode"}="mcoffee";
		$PG{"clustalo"}{"version"}="1.1.0";
		$PG{"clustalo"}{"binary"}="clustalo";
		$PG{"clustalo"}{"version"}="1.2.4";
		$PG{"strike"}{"4_TCOFFEE"}="STRIKE";
		$PG{"strike"}{"type"}="sequence_alignment_scoring";
		$PG{"strike"}{"ADDRESS"}="http://www.tcoffee.org/Projects/strike/index.html";
		@@ -1633,16 +1621,55 @@ $PG{"probcons"}{"source"}="http://probcons.stanford.edu/probcons_v1_12.tar.gz";
		$PG{"probcons"}{"mode"}="mcoffee";
		$PG{"probcons"}{"binary"}="probcons";
		$PG{"probcons"}{"version"}="1.12";
		$PG{"msaprobs"}{"4_TCOFFEE"}="MSAPROBS";
		$PG{"msaprobs"}{"type"}="sequence_multiple_aligner";
		$PG{"msaprobs"}{"ADDRESS"}="http://msaprobs.sourceforge.net/homepage.htm#latest";
		$PG{"msaprobs"}{"language2"}="CXX";
		$PG{"msaprobs"}{"language"}="C++";
		$PG{"msaprobs"}{"source"}="https://sourceforge.net/projects/msaprobs/files/MSAProbs-MPI/MSAProbs-MPI_rel1.0.5.tar.gz";
		$PG{"msaprobs"}{"mode"}="mcoffee";
		$PG{"msaprobs"}{"binary"}="msaprobs";
		$PG{"msaprobs"}{"version"}="1.05";
		$PG{"msaprobs"}{"update_action"}="never";
		$PG{"upp"}{"4_TCOFFEE"}="UPP";
		$PG{"upp"}{"type"}="sequence_multiple_aligner";
		$PG{"upp"}{"ADDRESS"}="http://www.cs.utexas.edu/users/phylo/software/upp/";
		$PG{"upp"}{"language2"}="CXX";
		$PG{"upp"}{"language"}="C++";
		$PG{"upp"}{"source"}="https://github.com/smirarab/pasta/archive/upp.zip";
		$PG{"upp"}{"mode"}="mcoffee";
		$PG{"upp"}{"binary"}="upp";
		$PG{"upp"}{"version"}="1";
		$PG{"upp"}{"update_action"}="never";
		$PG{"mafft"}{"4_TCOFFEE"}="MAFFT";
		$PG{"mafft"}{"type"}="sequence_multiple_aligner";
		$PG{"mafft"}{"ADDRESS"}="http://align.bmr.kyushu-u.ac.jp/mafft/online/server/";
		$PG{"mafft"}{"language"}="C";
		$PG{"mafft"}{"language"}="C";
		$PG{"mafft"}{"source"}="http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.603-with-extensions-src.tgz";
		$PG{"mafft"}{"windows"}="http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.603-mingw.tar";
		$PG{"mafft"}{"source"}="http://mafft.cbrc.jp/alignment/software/mafft-7.310-with-extensions-src.tgz";
		$PG{"mafft"}{"mode"}="mcoffee,rcoffee";
		$PG{"mafft"}{"binary"}="mafft.tar.gz";
		$PG{"mafft"}{"version"}="6.603";
		$PG{"mafft"}{"version"}="7.310";
		$PG{"msa"}{"4_TCOFFEE"}="MSA";
		$PG{"msa"}{"type"}="sequence_multiple_aligner";
		$PG{"msa"}{"ADDRESS"}="https://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/msa.html";
		$PG{"msa"}{"language"}="C";
		$PG{"msa"}{"language"}="C";
		$PG{"msa"}{"source"}="ftp://ftp.ncbi.nih.gov/pub/msa/msa.tar.Z";
		$PG{"msa"}{"mode"}="mcoffee";
		$PG{"msa"}{"binary"}="msa.pl";
		$PG{"msa"}{"version"}="1.0";
		$PG{"msa"}{"update_action"}="never";
		$PG{"dca"}{"4_TCOFFEE"}="DCA";
		$PG{"dca"}{"type"}="sequence_multiple_aligner";
		$PG{"dca"}{"ADDRESS"}="https://bibiserv2.cebitec.uni-bielefeld.de/dca";
		$PG{"dca"}{"language"}="C";
		$PG{"dca"}{"language"}="C";
		$PG{"dca"}{"source"}="https://bibiserv2.cebitec.uni-bielefeld.de/applications/dca/resources/downloads/dca-1.1-src.tar.gz";
		$PG{"dca"}{"mode"}="mcoffee";
		$PG{"dca"}{"binary"}="dca.pl";
		$PG{"dca"}{"version"}="1.1";
		$PG{"dca"}{"update_action"}="never";
		$PG{"muscle"}{"4_TCOFFEE"}="MUSCLE";
		$PG{"muscle"}{"type"}="sequence_multiple_aligner";
		$PG{"muscle"}{"ADDRESS"}="http://www.drive5.com/muscle/";
		@@ -1653,20 +1680,12 @@ $PG{"muscle"}{"windows"}="http://www.drive5.com/muscle/downloads3.7/muscle3.7_wi
		$PG{"muscle"}{"linux"}="http://www.drive5.com/muscle/downloads3.7/muscle3.7_linux_ia32.tar.gz";
		$PG{"muscle"}{"mode"}="mcoffee,rcoffee";
		$PG{"muscle"}{"version"}="3.7";
		$PG{"mus4"}{"4_TCOFFEE"}="MUS4";
		$PG{"mus4"}{"type"}="sequence_multiple_aligner";
		$PG{"mus4"}{"ADDRESS"}="http://www.drive5.com/muscle/";
		$PG{"mus4"}{"language"}="C++";
		$PG{"mus4"}{"language2"}="GPP";
		$PG{"mus4"}{"source"}="http://www.drive5.com/muscle/muscle4.0_src.tar.gz";
		$PG{"mus4"}{"mode"}="mcoffee,rcoffee";
		$PG{"mus4"}{"version"}="4.0";
		$PG{"pcma"}{"4_TCOFFEE"}="PCMA";
		$PG{"pcma"}{"type"}="sequence_multiple_aligner";
		$PG{"pcma"}{"ADDRESS"}="ftp://iole.swmed.edu/pub/PCMA/";
		$PG{"pcma"}{"ADDRESS"}="http://prodata.swmed.edu/pcma/pcma.php";
		$PG{"pcma"}{"language"}="C";
		$PG{"pcma"}{"language2"}="C";
		$PG{"pcma"}{"source"}="ftp://iole.swmed.edu/pub/PCMA/pcma.tar.gz";
		$PG{"pcma"}{"source"}="http://prodata.swmed.edu/download/pub/PCMA/pcma.tar.gz";
		$PG{"pcma"}{"mode"}="mcoffee";
		$PG{"pcma"}{"version"}="1.0";
		$PG{"kalign"}{"4_TCOFFEE"}="KALIGN";
		@@ -1682,9 +1701,10 @@ $PG{"amap"}{"type"}="sequence_multiple_aligner";
		$PG{"amap"}{"ADDRESS"}="http://bio.math.berkeley.edu/amap/";
		$PG{"amap"}{"language"}="C++";
		$PG{"amap"}{"language2"}="CXX";
		$PG{"amap"}{"source"}="http://amap-align.googlecode.com/files/amap.2.0.tar.gz";
		$PG{"amap"}{"source"}="https://github.com/mes5k/amap-align/archive/amap.zip";
		$PG{"amap"}{"mode"}="mcoffee";
		$PG{"amap"}{"version"}="2.0";
		$PG{"amap"}{"update_action"}="never";
		$PG{"proda"}{"4_TCOFFEE"}="PRODA";
		$PG{"proda"}{"type"}="sequence_multiple_aligner";
		$PG{"proda"}{"ADDRESS"}="http://proda.stanford.edu";
		@@ -1693,14 +1713,6 @@ $PG{"proda"}{"language2"}="CXX";
		$PG{"proda"}{"source"}="http://proda.stanford.edu/proda_1_0.tar.gz";
		$PG{"proda"}{"mode"}="mcoffee";
		$PG{"proda"}{"version"}="1.0";
		$PG{"fsa"}{"4_TCOFFEE"}="FSA";
		$PG{"fsa"}{"type"}="sequence_multiple_aligner";
		$PG{"fsa"}{"ADDRESS"}="http://fsa.sourceforge.net/";
		$PG{"fsa"}{"language"}="C++";
		$PG{"fsa"}{"language2"}="CXX";
		$PG{"fsa"}{"source"}="http://sourceforge.net/projects/fsa/files/fsa-1.15.3.tar.gz/download/";
		$PG{"fsa"}{"mode"}="mcoffee";
		$PG{"fsa"}{"version"}="1.15.3";
		$PG{"prank"}{"4_TCOFFEE"}="PRANK";
		$PG{"prank"}{"type"}="sequence_multiple_aligner";
		$PG{"prank"}{"ADDRESS"}="http://www.ebi.ac.uk/goldman-srv/prank/";
		@@ -1711,10 +1723,10 @@ $PG{"prank"}{"mode"}="mcoffee";
		$PG{"prank"}{"version"}="100303";
		$PG{"sap"}{"4_TCOFFEE"}="SAP";
		$PG{"sap"}{"type"}="structure_pairwise_aligner";
		$PG{"sap"}{"ADDRESS"}="http://mathbio.nimr.mrc.ac.uk/wiki/Software";
		$PG{"sap"}{"ADDRESS"}="https://mathbio.crick.ac.uk/wiki/Software#SAP";
		$PG{"sap"}{"language"}="C";
		$PG{"sap"}{"language2"}="C";
		$PG{"sap"}{"source"}="http://mathbio.nimr.mrc.ac.uk/download/SAP/sap-1.1.3.tar.gz";
		$PG{"sap"}{"source"}="https://github.com/jkleinj/SAP/archive/v.1.1.3.tar.gz";
		$PG{"sap"}{"mode"}="expresso,3dcoffee";
		$PG{"sap"}{"version"}="1.1.3";
		$PG{"TMalign"}{"4_TCOFFEE"}="TMALIGN";
		@@ -1728,12 +1740,12 @@ $PG{"TMalign"}{"mode"}="expresso,3dcoffee";
		$PG{"TMalign"}{"version"}="2013.05.11";
		$PG{"mustang"}{"4_TCOFFEE"}="MUSTANG";
		$PG{"mustang"}{"type"}="structure_pairwise_aligner";
		$PG{"mustang"}{"ADDRESS"}="http://www.cs.mu.oz.au/~arun/mustang";
		$PG{"mustang"}{"ADDRESS"}="http://lcb.infotech.monash.edu.au/mustang/";
		$PG{"mustang"}{"language"}="C++";
		$PG{"mustang"}{"language2"}="CXX";
		$PG{"mustang"}{"source"}="http://ww2.cs.mu.oz.au/~arun/mustang/mustang_v3.2.1.tgz";
		$PG{"mustang"}{"source"}="http://lcb.infotech.monash.edu.au/mustang/mustang_v3.2.3.tgz";
		$PG{"mustang"}{"mode"}="expresso,3dcoffee";
		$PG{"mustang"}{"version"}="3.2.1";
		$PG{"mustang"}{"version"}="3.2.3";
		$PG{"lsqman"}{"4_TCOFFEE"}="LSQMAN";
		$PG{"lsqman"}{"type"}="structure_pairwise_aligner";
		$PG{"lsqman"}{"ADDRESS"}="empty";
		@@ -1752,7 +1764,7 @@ $PG{"align_pdb"}{"update_action"}="never";
		$PG{"align_pdb"}{"mode"}="expresso,3dcoffee";
		$PG{"fugueali"}{"4_TCOFFEE"}="FUGUE";
		$PG{"fugueali"}{"type"}="structure_pairwise_aligner";
		$PG{"fugueali"}{"ADDRESS"}="http://www-cryst.bioc.cam.ac.uk/fugue/download.html";
		$PG{"fugueali"}{"ADDRESS"}="http://mizuguchilab.org/fugue/";
		$PG{"fugueali"}{"language"}="empty";
		$PG{"fugueali"}{"language2"}="empty";
		$PG{"fugueali"}{"source"}="empty";
		@@ -1785,26 +1797,28 @@ $PG{"sfold"}{"update_action"}="never";
		$PG{"sfold"}{"mode"}="rcoffee";
		$PG{"RNAplfold"}{"4_TCOFFEE"}="RNAPLFOLD";
		$PG{"RNAplfold"}{"type"}="RNA_secondarystructure_predictor";
		$PG{"RNAplfold"}{"ADDRESS"}="http://www.tbi.univie.ac.at/~ivo/RNA/";
		$PG{"RNAplfold"}{"ADDRESS"}="http://www.tbi.univie.ac.at/RNA/";
		$PG{"RNAplfold"}{"language"}="C";
		$PG{"RNAplfold"}{"language2"}="C";
		$PG{"RNAplfold"}{"source"}="http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-1.7.2.tar.gz";
		$PG{"RNAplfold"}{"source"}="http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-2.1.9.tar.gz";
		$PG{"RNAplfold"}{"mode"}="rcoffee,";
		$PG{"RNAplfold"}{"version"}="1.7.2";
		$PG{"RNAplfold"}{"binary"}="RNAplfold.tar.gz";
		$PG{"RNAplfold"}{"version"}="2.1.9";
		$PG{"retree"}{"4_TCOFFEE"}="PHYLIP";
		$PG{"retree"}{"type"}="RNA_secondarystructure_predictor";
		$PG{"retree"}{"type"}="Phylogeny";
		$PG{"retree"}{"ADDRESS"}="http://evolution.gs.washington.edu/phylip/";
		$PG{"retree"}{"language"}="C";
		$PG{"retree"}{"language2"}="C";
		$PG{"retree"}{"source"}="http://evolution.gs.washington.edu/phylip/download/phylip-3.69.tar.gz";
		$PG{"retree"}{"source"}="http://www.tcoffee.org/Packages/mirrors/source/phylip-3.66.tar.gz";
		$PG{"retree"}{"mode"}="trmsd,";
		$PG{"retree"}{"version"}="3.69";
		$PG{"retree"}{"binary"}="retree.tar.gz";
		$PG{"retree"}{"version"}="3.66";
		$PG{"hmmtop"}{"4_TCOFFEE"}="HMMTOP";
		$PG{"hmmtop"}{"type"}="protein_secondarystructure_predictor";
		$PG{"hmmtop"}{"ADDRESS"}="www.enzim.hu/hmmtop/";
		$PG{"hmmtop"}{"language"}="C";
		$PG{"hmmtop"}{"language2"}="C";
		$PG{"hmmtop"}{"source"}="empty";
		$PG{"hmmtop"}{"source"}="http://www.tcoffee.org/Packages/mirrors/hmmtop2.1.tgz";
		$PG{"hmmtop"}{"binary"}="hmmtop";
		$PG{"hmmtop"}{"update_action"}="never";
		$PG{"hmmtop"}{"mode"}="tcoffee";
		@@ -1814,7 +1828,7 @@ $PG{"gorIV"}{"type"}="protein_secondarystructure_predictor";
		$PG{"gorIV"}{"ADDRESS"}="http://mig.jouy.inra.fr/logiciels/gorIV/";
		$PG{"gorIV"}{"language"}="C";
		$PG{"gorIV"}{"language2"}="C";
		$PG{"gorIV"}{"source"}="http://mig.jouy.inra.fr/logiciels/gorIV/GOR_IV.tar.gz";
		$PG{"gorIV"}{"source"}="http://www.tcoffee.org/Packages/mirrors/GOR_IV.tar.gz";
		$PG{"gorIV"}{"update_action"}="never";
		$PG{"gorIV"}{"mode"}="tcoffee";
		$PG{"wublast.pl"}{"4_TCOFFEE"}="EBIWUBLASTc";
		@@ -1840,7 +1854,7 @@ $PG{"blastall"}{"type"}="protein_homology_predictor";
		$PG{"blastall"}{"ADDRESS"}="ftp://ftp.ncbi.nih.gov/blast/executables/LATEST";
		$PG{"blastall"}{"language"}="C";
		$PG{"blastall"}{"language2"}="C";
		$PG{"blastall"}{"source"}="empty";
		$PG{"blastall"}{"source"}="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-src.tar.gz";
		$PG{"blastall"}{"update_action"}="never";
		$PG{"blastall"}{"mode"}="psicoffee,expresso,3dcoffee";
		$PG{"legacy_blast.pl"}{"4_TCOFFEE"}="NCBIBLAST";
		@@ -1848,7 +1862,7 @@ $PG{"legacy_blast.pl"}{"type"}="protein_homology_predictor";
		$PG{"legacy_blast.pl"}{"ADDRESS"}="ftp://ftp.ncbi.nih.gov/blast/executables/LATEST";
		$PG{"legacy_blast.pl"}{"language"}="C";
		$PG{"legacy_blast.pl"}{"language2"}="C";
		$PG{"legacy_blast.pl"}{"source"}="empty";
		$PG{"legacy_blast.pl"}{"source"}="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-src.tar.gz";
		$PG{"legacy_blast.pl"}{"update_action"}="never";
		$PG{"legacy_blast.pl"}{"mode"}="psicoffee,expresso,3dcoffee";
		$PG{"SOAP::Lite"}{"4_TCOFFEE"}="SOAPLITE";
		@@ -1857,7 +1871,7 @@ $PG{"SOAP::Lite"}{"ADDRESS"}="http://cpansearch.perl.org/src/MKUTTER/SOAP-Lite-0
		$PG{"SOAP::Lite"}{"language"}="Perl";
		$PG{"SOAP::Lite"}{"language2"}="Perl";
		$PG{"SOAP::Lite"}{"source"}="empty";
		$PG{"blastpgp"}{"update_action"}="never";
		$PG{"SOAP::Lite"}{"update_action"}="never";
		$PG{"SOAP::Lite"}{"mode"}="none";
		$PG{"XML::Simple"}{"4_TCOFFEE"}="XMLSIMPLE";
		$PG{"XML::Simple"}{"type"}="library";
		@@ -1866,6 +1880,30 @@ $PG{"XML::Simple"}{"language"}="Perl";
		$PG{"XML::Simple"}{"language2"}="Perl";
		$PG{"XML::Simple"}{"source"}="empty";
		$PG{"XML::Simple"}{"mode"}="psicoffee,expresso,accurate";
		$PG{"x3dna"}{"4_TCOFFEE"}="x3dna-ssr";
		$PG{"x3dna"}{"type"}="RNA_secondarystructure_predictor";
		$PG{"x3dna"}{"ADDRESS"}="http://x3dna.bio.columbia.edu/";
		$PG{"x3dna"}{"source"}="http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz";
		$PG{"x3dna"}{"mode"}="saracoffee";
		$PG{"x3dna"}{"update_action"}="never";
		$PG{"fsa"}{"4_TCOFFEE"}="FSA";
		$PG{"fsa"}{"type"}="sequence_multiple_aligner";
		$PG{"fsa"}{"ADDRESS"}="http://fsa.sourceforge.net/";
		$PG{"fsa"}{"language"}="C++";
		$PG{"fsa"}{"language2"}="CXX";
		$PG{"fsa"}{"source"}="http://sourceforge.net/projects/fsa/files/fsa-1.15.3.tar.gz/download/";
		$PG{"fsa"}{"mode"}="mcoffee";
		$PG{"fsa"}{"version"}="1.15.3";
		$PG{"fsa"}{"update_action"}="never";
		$PG{"mus4"}{"4_TCOFFEE"}="MUS4";
		$PG{"mus4"}{"type"}="sequence_multiple_aligner";
		$PG{"mus4"}{"ADDRESS"}="http://www.drive5.com/muscle/";
		$PG{"mus4"}{"language"}="C++";
		$PG{"mus4"}{"language2"}="GPP";
		$PG{"mus4"}{"source"}="http://www.drive5.com/muscle/muscle4.0_src.tar.gz";
		$PG{"mus4"}{"mode"}="mcoffee,rcoffee";
		$PG{"mus4"}{"version"}="4.0";
		$PG{"mus4"}{"update_action"}="never";
		$MODE{"tcoffee"}{"name"}="tcoffee";
		$MODE{"rcoffee"}{"name"}="rcoffee";
		$MODE{"3dcoffee"}{"name"}="3dcoffee";

license.txt

+1 −1

Original line number	Diff line number	Diff line
		-------------------------------COPYRIGHT NOTICE------------------------------/
		ACADEMIC LICENCE AGREEMENT

		© Centro de Regulacio Genomica and Cedric Notredame ( 12 Aug 2014 - 22:07).
		© Centro de Regulacio Genomica and Cedric Notredame ( 11 Dec 2018 - 09:27).
		GNU GENERAL PUBLIC LICENSE
		Version 2, June 1991

t_coffee_source/coffee_defines.h

+12 −4

Original line number	Diff line number	Diff line
		@@ -2,7 +2,7 @@
		/* (c) Centro de Regulacio Genomica */
		/* and */
		/* Cedric Notredame */
		/* 12 Aug 2014 - 22:07. */
		/* 11 Dec 2018 - 09:27. */
		/All rights reserved. /
		/This file is part of T-COFFEE. /
		/* */
		@@ -21,7 +21,7 @@
		/* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA */
		/............................................... /
		/* If you need some more information */
		/* cedric.notredame@europe.com */
		/* cedric.notredame@gmail.com */
		/............................................... /
		/****************************COPYRIGHT NOTICE*****************************/
		#ifndef COFFEE_DEFINES_H
		@@ -59,6 +59,11 @@
		#define GIVE_MEMORY_BACK 0
		#define MEMSET0 1
		#define NO_MEMSET0 0
		#define MEMSET 1
		#define NOMEMSET -1
		#define RESIZE 1
		#define NORESIZE -1

		/OUTPUT DEFINITIONS/
		#define NO_COLOR_RESIDUE 127
		#define NO_COLOR_GAP 126
		@@ -82,7 +87,7 @@
		#define NOTEMPLATES 0

		#define EXTEND 1
		#define RESIZE 2


		#define SEN 0
		#define SPE 1
		@@ -275,7 +280,7 @@
		#define MAX_N_LIST 100

		#define COMMENT_SIZE 1000
		#define MAXNAMES 100
		#define MAXNAMES 1000
		#define FILENAMELEN 500 /* Max. file name length */
		#define MAX_N_PARAM 2000
		#define MAX_PARAM_LEN 200
		@@ -411,4 +416,7 @@
		#define NULL_6 NULL_4,NULL_2
		#define NULL_7 NULL_5,NULL_2


		#define PATCH_PRF ""
		//This variable is set so as to compensate a bug in Clustal-Omega
		#endif // -- COFFEE_DEFINES_H

t_coffee_source/data_headers/perl_header_lib.h

+2 −2

Original line number	Diff line number	Diff line
		@@ -2,7 +2,7 @@
		/* (c) Centro de Regulacio Genomica */
		/* and */
		/* Cedric Notredame */
		/* 12 Aug 2014 - 22:07. */
		/* 11 Dec 2018 - 09:27. */
		/All rights reserved. /
		/This file is part of T-COFFEE. /
		/* */
		@@ -21,7 +21,7 @@
		/* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA */
		/............................................... /
		/* If you need some more information */
		/* cedric.notredame@europe.com */
		/* cedric.notredame@gmail.com */
		/............................................... /
		/****************************COPYRIGHT NOTICE*****************************/
		/*