binaries/src/tcoffee/tclinkdb.txt

   1 PG t_coffee 4_TCOFFEE           TCOFFEE
   2 PG t_coffee type                sequence_multiple_aligner
   3 PG t_coffee ADDRESS             http://www.tcoffee.org
   4 PG t_coffee language            C
   5 PG t_coffee language2           C
   6 PG t_coffee source              http://www.tcoffee.org/Packages/T-COFFEE_distribution.tar.gz
   7 PG t_coffee update_action       always
   8 PG t_coffee mode                tcoffee,mcoffee,rcoffee,expresso,3dcoffee
   9
  10
  11 PG clustalw2 4_TCOFFEE          CLUSTALW2
  12 PG clustalw2 type               sequence_multiple_aligner
  13 PG clustalw2 ADDRESS            http://www.clustal.org
  14 PG clustalw2 language           C++
  15 PG clustalw2 language2          CXX
  16 PG clustalw2 source             http://www.clustal.org/download/2.0.10/clustalw-2.0.10-src.tar.gz
  17 PG clustalw2 mode               mcoffee,rcoffee
  18
  19 PG clustalw 4_TCOFFEE           CLUSTALW
  20 PG clustalw type                sequence_multiple_aligner
  21 PG clustalw ADDRESS             http://www.clustal.org
  22 PG clustalw language            C
  23 PG clustalw language2           C
  24 PG clustalw source              http://www.clustal.org/download/1.X/ftp-igbmc.u-strasbg.fr/pub/ClustalW/clustalw1.82.UNIX.tar.gz
  25 PG clustalw mode                mcoffee,rcoffee
  26
  27 PG dialign-t 4_TCOFFEE          DIALIGNT
  28 PG dialign-t type               sequence_multiple_aligner
  29 PG dialign-t ADDRESS            http://dialign-tx.gobics.de/
  30 PG dialign-t DIR                /usr/share/dialign-tx/
  31 PG dialign-t language           C
  32 PG dialign-t language2          C
  33 PG dialign-t source             http://dialign-tx.gobics.de/DIALIGN-TX_1.0.1.tar.gz
  34 PG dialign-t mode               mcoffee
  35 PG dialign-t binary             dialign-t
  36
  37 PG dialign-tx 4_TCOFFEE         DIALIGNTX
  38 PG dialign-tx type              sequence_multiple_aligner
  39 PG dialign-tx ADDRESS           http://dialign-tx.gobics.de/
  40 PG dialign-tx DIR               /usr/share/dialign-tx/
  41 PG dialign-tx language          C
  42 PG dialign-tx language2         C
  43 PG dialign-tx source            http://dialign-tx.gobics.de/DIALIGN-TX_1.0.1.tar.gz
  44 PG dialign-tx mode              mcoffee
  45 PG dialign-tx binary            dialign-tx
  46
  47 PG poa 4_TCOFFEE                POA
  48 PG poa type                     sequence_multiple_aligner
  49 PG poa ADDRESS                  http://www.bioinformatics.ucla.edu/poa/
  50 PG poa language                 C
  51 PG poa language2                C
  52 PG poa source                   http://downloads.sourceforge.net/poamsa/poaV2.tar.gz
  53 PG poa DIR                      /usr/share/
  54 PG poa FILE1                    blosum80.mat
  55 PG poa mode                     mcoffee
  56 PG poa binary                   poa
  57
  58 PG probcons 4_TCOFFEE           PROBCONS
  59 PG probcons type                sequence_multiple_aligner
  60 PG probcons ADDRESS             http://probcons.stanford.edu/
  61 PG probcons language2           CXX
  62 PG probcons language            C++
  63 PG probcons source              http://probcons.stanford.edu/probcons_v1_12.tar.gz
  64 PG probcons mode                mcoffee
  65 PG probcons binary              probcons
  66
  67 PG mafft 4_TCOFFEE              MAFFT
  68 PG mafft type                   sequence_multiple_aligner
  69 PG mafft ADDRESS                http://align.bmr.kyushu-u.ac.jp/mafft/online/server/
  70 PG mafft language               C
  71 PG mafft language               C
  72 PG mafft source                 http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.603-with-extensions-src.tgz
  73 PG mafft windows                http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.603-mingw.tar
  74 PG mafft mode                   mcoffee,rcoffee
  75 PG mafft binary                 mafft.tar.gz
  76
  77 PG muscle 4_TCOFFEE             MUSCLE
  78 PG muscle type                  sequence_multiple_aligner
  79 PG muscle ADDRESS               http://www.drive5.com/muscle/
  80 PG muscle language              C++
  81 PG muscle language2             GPP
  82 PG muscle source                http://www.drive5.com/muscle/downloads3.6/muscle3.6_src.tar.gz
  83 PG muscle windows               http://www.drive5.com/muscle/downloads3.6/muscle3.6_win32.zip
  84 PG muscle linux                 http://www.drive5.com/muscle/downloads3.6/muscle3.6_linux_ia32.tar.gz
  85 PG muscle mode                  mcoffee,rcoffee
  86
  87
  88 PG pcma 4_TCOFFEE               PCMA
  89 PG pcma type                    sequence_multiple_aligner
  90 PG pcma ADDRESS                 ftp://iole.swmed.edu/pub/PCMA/
  91 PG pcma language                C
  92 PG pcma language2               C
  93 PG pcma source                  ftp://iole.swmed.edu/pub/PCMA/pcma.tar.gz
  94 PG pcma mode                    mcoffee
  95
  96 PG kalign 4_TCOFFEE             KALIGN
  97 PG kalign type                  sequence_multiple_aligner
  98 PG kalign ADDRESS               http://msa.cgb.ki.se
  99 PG kalign language              C
 100 PG kalign language2             C
 101 PG kalign source                http://msa.cgb.ki.se/downloads/kalign/current.tar.gz
 102 PG kalign mode                  mcoffee
 103
 104
 105 PG amap 4_TCOFFEE               AMAP
 106 PG amap type                    sequence_multiple_aligner
 107 PG amap ADDRESS                 http://bio.math.berkeley.edu/amap/
 108 PG amap language                C++
 109 PG amap language2               CXX
 110 PG amap source                  http://baboon.math.berkeley.edu/amap/download/amap.2.2.tar.gz
 111 PG amap mode                    mcoffee
 112
 113
 114 PG proda 4_TCOFFEE              PRODA
 115 PG proda type                   sequence_multiple_aligner
 116 PG proda ADDRESS                http://proda.stanford.edu
 117 PG proda language               C++
 118 PG proda language2              CXX
 119 PG proda source                 http://proda.stanford.edu/proda_1_0.tar.gz
 120 PG proda mode                   mcoffee
 121
 122 PG prank 4_TCOFFEE              PRANK
 123 PG prank type                   sequence_multiple_aligner
 124 PG prank ADDRESS                http://www.ebi.ac.uk/goldman-srv/prank/
 125 PG prank language               C++
 126 PG prank language2              CXX
 127 PG prank source                 http://www.ebi.ac.uk/goldman-srv/prank/src/old/prank.src.081202.tgz
 128 PG prank mode                   mcoffee
 129
 130 PG sap 4_TCOFFEE                        SAP
 131 PG sap type                     structure_pairwise_aligner
 132 PG sap ADDRESS                  http://mathbio.nimr.mrc.ac.uk/wiki/Software
 133 PG sap language                 C
 134 PG sap language2                C
 135 PG sap source                   http://www.tcoffee.org/Packages/sap_distribution_TCC_0.6.tar.gz
 136 PG sap mode                     expresso,3dcoffee
 137
 138 PG TMalign 4_TCOFFEE            TMALIGN
 139 PG TMalign type                 structure_pairwise_aligner
 140 PG TMalign ADDRESS              http://zhang.bioinformatics.ku.edu/TM-align/TMalign.f
 141 PG TMalign language             Fortran
 142 PG TMalign language2            Fortran
 143 PG TMalign source               http://zhang.bioinformatics.ku.edu/TM-align/TMalign.f
 144 PG TMalign linux                http://zhang.bioinformatics.ku.edu/TM-align/TMalign_32.gz
 145 PG TMalign mode                 expresso,3dcoffee
 146
 147
 148 PG mustang 4_TCOFFEE            MUSTANG
 149 PG mustang type                 structure_pairwise_aligner
 150 PG mustang ADDRESS              http://www.cs.mu.oz.au/~arun/mustang
 151 PG mustang language             C++
 152 PG mustang language2            CXX
 153 PG mustang source               http://www.cs.mu.oz.au/~arun/mustang/mustang_v.3.tgz
 154 PG mustang mode                 expresso,3dcoffee
 155
 156 PG lsqman 4_TCOFFEE             LSQMAN
 157 PG lsqman type                  structure_pairwise_aligner
 158 PG lsqman ADDRESS               empty
 159 PG lsqman language              empty
 160 PG lsqman language2             empty
 161 PG lsqman source                empty
 162 PG lsqman update_action         never
 163 PG lsqman mode                  expresso,3dcoffee
 164
 165 PG align_pdb 4_TCOFFEE          ALIGN_PDB
 166 PG align_pdb type               structure_pairwise_aligner
 167 PG align_pdb ADDRESS            empty
 168 PG align_pdb language           empty
 169 PG align_pdb language2          empty
 170 PG align_pdb source             empty
 171 PG align_pdb update_action      never
 172 PG align_pdb mode               expresso,3dcoffee
 173
 174
 175 PG fugueali 4_TCOFFEE           FUGUE
 176 PG fugueali type                structure_pairwise_aligner
 177 PG fugueali ADDRESS             http://www-cryst.bioc.cam.ac.uk/fugue/download.html
 178 PG fugueali language            empty
 179 PG fugueali language2           empty
 180 PG fugueali source              empty
 181 PG fugueali update_action       never
 182 PG fugueali mode                expresso,3dcoffee
 183
 184 PG dalilite.pl 4_TCOFFEE        DALILITEc
 185 PG dalilite.pl type             structure_pairwise_aligner
 186 PG dalilite.pl ADDRESS          built_in
 187 PG dalilite.pl ADDRESS2         http://www.ebi.ac.uk/Tools/webservices/services/dalilite
 188 PG dalilite.pl language         Perl
 189 PG dalilite.pl language2        Perl
 190 PG dalilite.pl source           empty
 191 PG dalilite.pl update_action    never
 192 PG dalilite.pl mode             expresso,3dcoffee
 193
 194 PG probconsRNA 4_TCOFFEE        PROBCONSRNA
 195 PG probconsRNA type             RNA_multiple_aligner
 196 PG probconsRNA ADDRESS          http://probcons.stanford.edu/
 197 PG probconsRNA language         C++
 198 PG probconsRNA language2        CXX
 199 PG probconsRNA source           http://probcons.stanford.edu/probconsRNA.tar.gz
 200 PG probconsRNA mode             mcoffee,rcoffee
 201
 202 PG sfold 4_TCOFFEE              CONSAN
 203 PG sfold type                   RNA_pairwise_aligner
 204 PG sfold ADDRESS                http://selab.janelia.org/software/consan/
 205 PG sfold language               empty
 206 PG sfold language2              empty
 207 PG sfold source                 empty
 208 PG sfold update_action          never
 209 PG sfold mode                   rcoffee
 210
 211 PG RNAplfold 4_TCOFFEE          RNAPLFOLD
 212 PG RNAplfold type               RNA_secondarystructure_predictor
 213 PG RNAplfold ADDRESS            http://www.tbi.univie.ac.at/~ivo/RNA/
 214 PG RNAplfold language           C
 215 PG RNAplfold language2          C
 216 PG RNAplfold source             http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-1.7.2.tar.gz
 217 PG RNAplfold mode               rcoffee
 218
 219 PG hmmtop 4_TCOFFEE             HMMTOP
 220 PG hmmtop type                  protein_secondarystructure_predictor
 221 PG hmmtop ADDRESS               www.enzim.hu/hmmtop/
 222 PG hmmtop language              C
 223 PG hmmtop language2             C
 224 PG hmmtop source                empty
 225 PG hmmtop update_action         never
 226 PG hmmtop mode                  tcoffee
 227
 228 PG gorIV 4_TCOFFEE              GOR4
 229 PG gorIV type                   protein_secondarystructure_predictor
 230 PG gorIV ADDRESS                http://mig.jouy.inra.fr/logiciels/gorIV/
 231 PG gorIV language               C
 232 PG gorIV language2              C
 233 PG gorIV source                 http://mig.jouy.inra.fr/logiciels/gorIV/GOR_IV.tar.gz
 234 PG gorIV update_action          never
 235 PG gorIV mode                   tcoffee
 236
 237 PG wublast.pl 4_TCOFFEE         EBIWUBLASTc
 238 PG wublast.pl type              protein_homology_predictor
 239 PG wublast.pl ADDRESS           built_in
 240 PG wublast.pl ADDRESS2          http://www.ebi.ac.uk/Tools/webservices/services/wublast
 241 PG wublast.pl language          Perl
 242 PG wublast.pl language2         Perl
 243 PG wublast.pl source            empty
 244 PG wublast.pl update_action     never
 245 PG wublast.pl mode              psicoffee,expresso,3dcoffee
 246
 247 PG blastpgp.pl 4_TCOFFEE        EBIBLASTPGPc
 248 PG blastpgp.pl type             protein_homology_predictor
 249 PG blastpgp.pl ADDRESS          built_in
 250 PG blastpgp.pl ADDRESS2         http://www.ebi.ac.uk/Tools/webservices/services/blastpgp
 251 PG blastpgp.pl language         Perl
 252 PG blastpgp.pl language2        Perl
 253 PG blastpgp.pl source           empty
 254 PG blastpgp.pl update_action    never
 255 PG blastpgp.pl mode             psicoffee,expresso,3dcoffee
 256
 257
 258 PG blastcl3 4_TCOFFEE           NCBIWEBBLAST
 259 PG blastcl3 type                protein_homology_predictor
 260 PG blastcl3 ADDRESS             ftp://ftp.ncbi.nih.gov/blast/executables/LATEST
 261 PG blastcl3 language            C
 262 PG blastcl3 language2           C
 263 PG blastcl3 source              empty
 264 PG blastcl3 update_action       never
 265 PG blastcl3 mode                psicoffee,expresso,3dcoffee
 266
 267
 268 PG blastpgp 4_TCOFFEE           NCBIBLAST
 269 PG blastpgp type                protein_homology_predictor
 270 PG blastpgp ADDRESS             ftp://ftp.ncbi.nih.gov/blast/executables/LATEST
 271 PG blastpgp language            C
 272 PG blastpgp language2           C
 273 PG blastpgp source              empty
 274 PG blastpgp update_action       never
 275 PG blastpgp mode                psicoffee,expresso,3dcoffee
 276
 277 PG SOAP::Lite 4_TCOFFEE         SOAPLITE
 278 PG SOAP::Lite type              library
 279 PG SOAP::Lite ADDRESS           http://cpansearch.perl.org/src/MKUTTER/SOAP-Lite-0.710.08/Makefile.PL
 280 PG SOAP::Lite language          Perl
 281 PG SOAP::Lite language2         Perl
 282 PG SOAP::Lite source            empty
 283 PG SOAP::Lite mode              psicoffee,expresso,3dcoffee
 284
 285
 286 MODE tcoffee  name tcoffee
 287 MODE rcoffee  name rcoffee
 288 MODE 3dcoffee name 3dcoffee
 289 MODE mcoffee  name mcoffee
 290 MODE expresso name expresso