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 CXX 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 clustalo 4_TCOFFEE CLUSTALO 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 mode mcoffee PG clustalo version 1.1.0 PG strike 4_TCOFFEE STRIKE PG strike type sequence_alignment_scoring PG strike ADDRESS http://www.tcoffee.org/Projects/strike/index.html PG strike language C++ PG strike language2 CXX PG strike source http://www.tcoffee.org/Projects/strike/strike_v1.2.tar.bz2 PG strike mode tcoffee,expresso PG strike version 1.2 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.100802.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/sap-1.1.3.tar.gz PG sap mode expresso,3dcoffee PG sap version 1.1.3 PG TMalign 4_TCOFFEE TMALIGN PG TMalign type structure_pairwise_aligner PG TMalign ADDRESS http://zhanglab.ccmb.med.umich.edu/TM-align/TMalign.f PG TMalign language Fortran PG TMalign language2 Fortran PG TMalign source http://zhanglab.ccmb.med.umich.edu/TM-align/TMalign.f PG TMalign linux http://zhanglab.ccmb.med.umich.edu/TM-align/TMalign_32.gz 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 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 binary hmmtop PG hmmtop update_action never PG hmmtop mode tcoffee PG hmmtop version 2.1 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 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