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/sources/tcoffee/stable/T-COFFEE_distribution.tar.gz
PG t_coffee update_action	always
PG t_coffee binary              t_coffee
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-1.2.4.tar.gz
PG clustalo mode		mcoffee
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
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 strike binary		strike

     
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 binary		clustalw2
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 clustalw binary		clustalw

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 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://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		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/
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 pcma 4_TCOFFEE		PCMA
PG pcma type			sequence_multiple_aligner		
PG pcma ADDRESS			http://prodata.swmed.edu/pcma/pcma.php
PG pcma language		C
PG pcma language2		C	
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
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			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
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 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			https://mathbio.crick.ac.uk/wiki/Software#SAP
PG sap language			C
PG sap language2		C	
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 sap binary			sap

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://lcb.infotech.monash.edu.au/mustang/
PG mustang language		C++
PG mustang language2		CXX
PG mustang source		http://lcb.infotech.monash.edu.au/mustang/mustang_v3.2.3.tgz
PG mustang mode			expresso,3dcoffee	  
PG mustang version		3.2.3  

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://mizuguchilab.org/fugue/
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/RNA/
PG RNAplfold language	C
PG RNAplfold language2	C
PG RNAplfold source		http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-2.1.9.tar.gz	
PG RNAplfold mode		rcoffee, seq_reformat
PG RNAplfold binary             RNAplfold.tar.gz
PG RNAplfold version	2.1.9

PG retree 4_TCOFFEE		PHYLIP
PG retree type			Phylogeny Reconstruction
PG retree ADDRESS		http://evolution.gs.washington.edu/phylip/
PG retree language		C
PG retree language2		C
PG retree source		http://www.tcoffee.org/Packages/mirrors/source/phylip-3.66.tar.gz
PG retree  mode			trmsd, seq_reformat
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		http://www.tcoffee.org/Packages/mirrors/hmmtop2.1.tgz
PG hmmtop binary		hmmtop
PG hmmtop update_action		never
PG hmmtop mode			psicoffee
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://www.tcoffee.org/Packages/mirrors/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		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
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	 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
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 SOAP::Lite 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


PG x3dna       4_TCOFFEE	x3dna
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
MODE mcoffee  name mcoffee
MODE expresso name expresso
MODE trmsd    name trmsd
MODE accurate name accurate
MODE seq_reformat name seq_reformat
