--- /dev/null
+PG t_coffee 4_TCOFFEE TCOFFEE
+PG t_coffee type sequence_multiple_aligner
+PG t_coffee ADDRESS http://www.tcoffee.org
+PG t_coffee language C
+PG t_coffee language2 C
+PG t_coffee source http://www.tcoffee.org/Packages/T-COFFEE_distribution.tar.gz
+PG t_coffee update_action always
+PG t_coffee mode tcoffee,mcoffee,rcoffee,expresso,3dcoffee
+
+
+PG clustalw2 4_TCOFFEE CLUSTALW2
+PG clustalw2 type sequence_multiple_aligner
+PG clustalw2 ADDRESS http://www.clustal.org
+PG clustalw2 language C++
+PG clustalw2 language2 CXX
+PG clustalw2 source http://www.clustal.org/download/2.0.10/clustalw-2.0.10-src.tar.gz
+PG clustalw2 mode mcoffee,rcoffee
+PG clustalw2 version 2.0.10
+
+PG clustalw 4_TCOFFEE CLUSTALW
+PG clustalw type sequence_multiple_aligner
+PG clustalw ADDRESS http://www.clustal.org
+PG clustalw language C
+PG clustalw language2 C
+PG clustalw source http://www.clustal.org/download/1.X/ftp-igbmc.u-strasbg.fr/pub/ClustalW/clustalw1.82.UNIX.tar.gz
+PG clustalw mode mcoffee,rcoffee
+PG clustalw version 1.82
+
+PG dialign-t 4_TCOFFEE DIALIGNT
+PG dialign-t type sequence_multiple_aligner
+PG dialign-t ADDRESS http://dialign-tx.gobics.de/
+PG dialign-t DIR /usr/share/dialign-tx/
+PG dialign-t language C
+PG dialign-t language2 C
+PG dialign-t source http://dialign-tx.gobics.de/DIALIGN-TX_1.0.2.tar.gz
+PG dialign-t mode mcoffee
+PG dialign-t binary dialign-t
+PG dialign-t version 1.0.2
+
+PG dialign-tx 4_TCOFFEE DIALIGNTX
+PG dialign-tx type sequence_multiple_aligner
+PG dialign-tx ADDRESS http://dialign-tx.gobics.de/
+PG dialign-tx DIR /usr/share/dialign-tx/
+PG dialign-tx language C
+PG dialign-tx language2 C
+PG dialign-tx source http://dialign-tx.gobics.de/DIALIGN-TX_1.0.2.tar.gz
+PG dialign-tx mode mcoffee
+PG dialign-tx binary dialign-tx
+PG dialign-tx version 1.0.2
+
+PG poa 4_TCOFFEE POA
+PG poa type sequence_multiple_aligner
+PG poa ADDRESS http://www.bioinformatics.ucla.edu/poa/
+PG poa language C
+PG poa language2 C
+PG poa source http://downloads.sourceforge.net/poamsa/poaV2.tar.gz
+PG poa DIR /usr/share/
+PG poa FILE1 blosum80.mat
+PG poa mode mcoffee
+PG poa binary poa
+PG poa version 2.0
+
+PG probcons 4_TCOFFEE PROBCONS
+PG probcons type sequence_multiple_aligner
+PG probcons ADDRESS http://probcons.stanford.edu/
+PG probcons language2 CXX
+PG probcons language C++
+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 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 mode mcoffee,rcoffee
+PG mafft binary mafft.tar.gz
+PG mafft version 6.603
+
+PG muscle 4_TCOFFEE MUSCLE
+PG muscle type sequence_multiple_aligner
+PG muscle ADDRESS http://www.drive5.com/muscle/
+PG muscle language C++
+PG muscle language2 GPP
+PG muscle source http://www.drive5.com/muscle/downloads3.7/muscle3.7_src.tar.gz
+PG muscle windows http://www.drive5.com/muscle/downloads3.7/muscle3.7_win32.zip
+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 language C
+PG pcma language2 C
+PG pcma source ftp://iole.swmed.edu/pub/PCMA/pcma.tar.gz
+PG pcma mode mcoffee
+PG pcma version 1.0
+
+PG kalign 4_TCOFFEE KALIGN
+PG kalign type sequence_multiple_aligner
+PG kalign ADDRESS http://msa.cgb.ki.se
+PG kalign language C
+PG kalign language2 C
+PG kalign source http://msa.cgb.ki.se/downloads/kalign/current.tar.gz
+PG kalign mode mcoffee
+PG kalign version 1.0
+
+
+PG amap 4_TCOFFEE AMAP
+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 mode mcoffee
+PG amap version 2.0
+
+
+PG proda 4_TCOFFEE PRODA
+PG proda type sequence_multiple_aligner
+PG proda ADDRESS http://proda.stanford.edu
+PG proda language C++
+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/
+PG prank language C++
+PG prank language2 CXX
+PG prank source http://www.ebi.ac.uk/goldman-srv/prank/src/prank/prank.src.100303.tgz
+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 language C
+PG sap language2 C
+PG sap source http://mathbio.nimr.mrc.ac.uk/download/sap-1.1.1.tar.gz
+PG sap mode expresso,3dcoffee
+PG sap version 1.1.1
+
+PG TMalign 4_TCOFFEE TMALIGN
+PG TMalign type structure_pairwise_aligner
+PG TMalign ADDRESS http://zhang.bioinformatics.ku.edu/TM-align/TMalign.f
+PG TMalign language Fortran
+PG TMalign language2 Fortran
+PG TMalign source http://zhang.bioinformatics.ku.edu/TM-align/TMalign.f
+PG TMalign linux http://zhang.bioinformatics.ku.edu/TM-align/TMalign_32.gz
+PG TMalign mode expresso,3dcoffee
+PG TMalign version 1.0
+
+
+PG mustang 4_TCOFFEE MUSTANG
+PG mustang type structure_pairwise_aligner
+PG mustang ADDRESS http://www.cs.mu.oz.au/~arun/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 mode expresso,3dcoffee
+PG mustang version 3.2.1
+
+PG lsqman 4_TCOFFEE LSQMAN
+PG lsqman type structure_pairwise_aligner
+PG lsqman ADDRESS empty
+PG lsqman language empty
+PG lsqman language2 empty
+PG lsqman source empty
+PG lsqman update_action never
+PG lsqman mode expresso,3dcoffee
+
+PG align_pdb 4_TCOFFEE ALIGN_PDB
+PG align_pdb type structure_pairwise_aligner
+PG align_pdb ADDRESS empty
+PG align_pdb language empty
+PG align_pdb language2 empty
+PG align_pdb source empty
+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 language empty
+PG fugueali language2 empty
+PG fugueali source empty
+PG fugueali update_action never
+PG fugueali mode expresso,3dcoffee
+
+PG dalilite.pl 4_TCOFFEE DALILITEc
+PG dalilite.pl type structure_pairwise_aligner
+PG dalilite.pl ADDRESS built_in
+PG dalilite.pl ADDRESS2 http://www.ebi.ac.uk/Tools/webservices/services/dalilite
+PG dalilite.pl language Perl
+PG dalilite.pl language2 Perl
+PG dalilite.pl source empty
+PG dalilite.pl update_action never
+PG dalilite.pl mode expresso,3dcoffee
+
+PG probconsRNA 4_TCOFFEE PROBCONSRNA
+PG probconsRNA type RNA_multiple_aligner
+PG probconsRNA ADDRESS http://probcons.stanford.edu/
+PG probconsRNA language C++
+PG probconsRNA language2 CXX
+PG probconsRNA source http://probcons.stanford.edu/probconsRNA.tar.gz
+PG probconsRNA mode mcoffee,rcoffee
+PG probconsRNA version 1.0
+
+PG sfold 4_TCOFFEE CONSAN
+PG sfold type RNA_pairwise_aligner
+PG sfold ADDRESS http://selab.janelia.org/software/consan/
+PG sfold language empty
+PG sfold language2 empty
+PG sfold source empty
+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 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 mode rcoffee, seq_reformat
+PG RNAplfold version 1.7.2
+
+PG retree 4_TCOFFEE PHYLIP
+PG retree type RNA_secondarystructure_predictor
+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 mode trmsd, seq_reformat
+PG retree version 3.69
+
+
+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 update_action never
+PG hmmtop mode tcoffee
+
+PG gorIV 4_TCOFFEE GOR4
+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 update_action never
+PG gorIV mode tcoffee
+
+PG wublast.pl 4_TCOFFEE EBIWUBLASTc
+PG wublast.pl type protein_homology_predictor
+PG wublast.pl ADDRESS built_in
+PG wublast.pl ADDRESS2 http://www.ebi.ac.uk/Tools/webservices/services/wublast
+PG wublast.pl language Perl
+PG wublast.pl language2 Perl
+PG wublast.pl source empty
+PG wublast.pl update_action never
+PG wublast.pl mode psicoffee,expresso,accurate
+
+PG blastpgp.pl 4_TCOFFEE EBIBLASTPGPc
+PG blastpgp.pl type protein_homology_predictor
+PG blastpgp.pl ADDRESS built_in
+PG blastpgp.pl ADDRESS2 http://www.ebi.ac.uk/Tools/webservices/services/blastpgp
+PG blastpgp.pl language Perl
+PG blastpgp.pl language2 Perl
+PG blastpgp.pl source empty
+PG blastpgp.pl update_action never
+PG blastpgp.pl mode psicoffee,expresso,accurate
+
+
+PG blastcl3 4_TCOFFEE NCBIWEBBLAST
+PG blastcl3 type protein_homology_predictor
+PG blastcl3 ADDRESS ftp://ftp.ncbi.nih.gov/blast/executables/LATEST
+PG blastcl3 language C
+PG blastcl3 language2 C
+PG blastcl3 source empty
+PG blastcl3 update_action never
+PG blastcl3 mode psicoffee,expresso,3dcoffee
+
+PG blastall 4_TCOFFEE blastall
+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 update_action never
+PG blastall mode psicoffee,expresso,3dcoffee
+
+PG legacy_blast.pl 4_TCOFFEE NCBIBLAST
+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 update_action never
+PG legacy_blast.pl mode psicoffee,expresso,3dcoffee
+
+PG SOAP::Lite 4_TCOFFEE SOAPLITE
+PG SOAP::Lite type library
+PG SOAP::Lite ADDRESS http://cpansearch.perl.org/src/MKUTTER/SOAP-Lite-0.710.08/Makefile.PL
+PG SOAP::Lite language Perl
+PG SOAP::Lite language2 Perl
+PG SOAP::Lite source empty
+PG blastpgp update_action never
+PG SOAP::Lite mode none
+
+PG XML::Simple 4_TCOFFEE XMLSIMPLE
+PG XML::Simple type library
+PG XML::Simple ADDRESS http://search.cpan.org/~grantm/XML-Simple-2.18/lib/XML/Simple.pm
+PG XML::Simple language Perl
+PG XML::Simple language2 Perl
+PG XML::Simple source empty
+PG XML::Simple mode psicoffee,expresso,accurate
+
+
+
+MODE tcoffee name tcoffee
+MODE rcoffee name rcoffee
+MODE 3dcoffee name 3dcoffee
+MODE mcoffee name mcoffee
+MODE expresso name expresso
+MODE trmsd name trmsd
+MODE accurate name accurate
+MODE seq_reformat name seq_reformat
git://source.jalview.org / jabaws.git / blobdiff