JWS-112 Bumping version of T-Coffee to version 11.00.8cbe486.

[jabaws.git] / binaries / src / tcoffee / tclinkdb.txt

diff --git a/binaries/src/tcoffee/tclinkdb.txt b/binaries/src/tcoffee/tclinkdb.txt
index 082f3f1..5207f8b 100644 (file)
--- a/binaries/src/tcoffee/tclinkdb.txt
+++ b/binaries/src/tcoffee/tclinkdb.txt
@@ -1,12 +1,29 @@
 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 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               
@@ -154,7 +171,7 @@ 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 source                        http://www.ebi.ac.uk/goldman-srv/prank/src/prank/prank.src.100802.tgz
 PG prank mode                  mcoffee     
 PG prank version               100303      
 
@@ -163,19 +180,19 @@ 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 source                  http://mathbio.nimr.mrc.ac.uk/download/SAP/sap-1.1.3.tar.gz
 PG sap mode                    expresso,3dcoffee
-PG sap version                 1.1.1
+PG sap version                 1.1.3
 
 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 ADDRESS             http://zhanglab.ccmb.med.umich.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 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             1.0         
+PG TMalign version             2013.05.11          
 
 
 PG mustang 4_TCOFFEE           MUSTANG
@@ -268,8 +285,10 @@ 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
@@ -300,16 +319,6 @@ 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