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 PG clustalw2 version    2.0.10
  19
  20 PG clustalw 4_TCOFFEE           CLUSTALW
  21 PG clustalw type                sequence_multiple_aligner
  22 PG clustalw ADDRESS             http://www.clustal.org
  23 PG clustalw language            C
  24 PG clustalw language2           C
  25 PG clustalw source              http://www.clustal.org/download/1.X/ftp-igbmc.u-strasbg.fr/pub/ClustalW/clustalw1.82.UNIX.tar.gz
  26 PG clustalw mode                mcoffee,rcoffee
  27 PG clustalw version             1.82
  28
  29 PG dialign-t 4_TCOFFEE          DIALIGNT
  30 PG dialign-t type               sequence_multiple_aligner
  31 PG dialign-t ADDRESS            http://dialign-tx.gobics.de/
  32 PG dialign-t DIR                /usr/share/dialign-tx/
  33 PG dialign-t language           C
  34 PG dialign-t language2          C
  35 PG dialign-t source             http://dialign-tx.gobics.de/DIALIGN-TX_1.0.2.tar.gz
  36 PG dialign-t mode               mcoffee
  37 PG dialign-t binary             dialign-t
  38 PG dialign-t version    1.0.2
  39
  40 PG dialign-tx 4_TCOFFEE         DIALIGNTX
  41 PG dialign-tx type              sequence_multiple_aligner
  42 PG dialign-tx ADDRESS           http://dialign-tx.gobics.de/
  43 PG dialign-tx DIR               /usr/share/dialign-tx/
  44 PG dialign-tx language          C
  45 PG dialign-tx language2         C
  46 PG dialign-tx source            http://dialign-tx.gobics.de/DIALIGN-TX_1.0.2.tar.gz
  47 PG dialign-tx mode              mcoffee
  48 PG dialign-tx binary            dialign-tx
  49 PG dialign-tx version   1.0.2
  50
  51 PG poa 4_TCOFFEE                POA
  52 PG poa type                     sequence_multiple_aligner
  53 PG poa ADDRESS                  http://www.bioinformatics.ucla.edu/poa/
  54 PG poa language                 C
  55 PG poa language2                C
  56 PG poa source                   http://downloads.sourceforge.net/poamsa/poaV2.tar.gz
  57 PG poa DIR                      /usr/share/
  58 PG poa FILE1                    blosum80.mat
  59 PG poa mode                     mcoffee
  60 PG poa binary                   poa
  61 PG poa version                  2.0
  62
  63 PG probcons 4_TCOFFEE           PROBCONS
  64 PG probcons type                sequence_multiple_aligner
  65 PG probcons ADDRESS             http://probcons.stanford.edu/
  66 PG probcons language2           CXX
  67 PG probcons language            C++
  68 PG probcons source              http://probcons.stanford.edu/probcons_v1_12.tar.gz
  69 PG probcons mode                mcoffee
  70 PG probcons binary              probcons
  71 PG probcons version             1.12
  72
  73 PG mafft 4_TCOFFEE              MAFFT
  74 PG mafft type                   sequence_multiple_aligner
  75 PG mafft ADDRESS                http://align.bmr.kyushu-u.ac.jp/mafft/online/server/
  76 PG mafft language               C
  77 PG mafft language               C
  78 PG mafft source                 http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.603-with-extensions-src.tgz
  79 PG mafft windows                http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.603-mingw.tar
  80 PG mafft mode                   mcoffee,rcoffee
  81 PG mafft binary                 mafft.tar.gz
  82 PG mafft version                6.603
  83
  84 PG muscle 4_TCOFFEE             MUSCLE
  85 PG muscle type                  sequence_multiple_aligner
  86 PG muscle ADDRESS               http://www.drive5.com/muscle/
  87 PG muscle language              C++
  88 PG muscle language2             GPP
  89 PG muscle source                http://www.drive5.com/muscle/downloads3.7/muscle3.7_src.tar.gz
  90 PG muscle windows               http://www.drive5.com/muscle/downloads3.7/muscle3.7_win32.zip
  91 PG muscle linux                 http://www.drive5.com/muscle/downloads3.7/muscle3.7_linux_ia32.tar.gz
  92 PG muscle mode                  mcoffee,rcoffee
  93 PG muscle version               3.7
  94
  95 PG mus4 4_TCOFFEE               MUS4
  96 PG mus4 type                    sequence_multiple_aligner
  97 PG mus4 ADDRESS                 http://www.drive5.com/muscle/
  98 PG mus4 language                C++
  99 PG mus4 language2               GPP
 100 PG mus4 source                  http://www.drive5.com/muscle/muscle4.0_src.tar.gz
 101 PG mus4 mode                    mcoffee,rcoffee
 102 PG mus4 version                 4.0
 103
 104
 105 PG pcma 4_TCOFFEE               PCMA
 106 PG pcma type                    sequence_multiple_aligner
 107 PG pcma ADDRESS                 ftp://iole.swmed.edu/pub/PCMA/
 108 PG pcma language                C
 109 PG pcma language2               C
 110 PG pcma source                  ftp://iole.swmed.edu/pub/PCMA/pcma.tar.gz
 111 PG pcma mode                    mcoffee
 112 PG pcma version                 1.0
 113
 114 PG kalign 4_TCOFFEE             KALIGN
 115 PG kalign type                  sequence_multiple_aligner
 116 PG kalign ADDRESS               http://msa.cgb.ki.se
 117 PG kalign language              C
 118 PG kalign language2             C
 119 PG kalign source                http://msa.cgb.ki.se/downloads/kalign/current.tar.gz
 120 PG kalign mode                  mcoffee
 121 PG kalign version               1.0
 122
 123
 124 PG amap 4_TCOFFEE               AMAP
 125 PG amap type                    sequence_multiple_aligner
 126 PG amap ADDRESS                 http://bio.math.berkeley.edu/amap/
 127 PG amap language                C++
 128 PG amap language2               CXX
 129 PG amap source                  http://amap-align.googlecode.com/files/amap.2.0.tar.gz
 130 PG amap mode                    mcoffee
 131 PG amap version                 2.0
 132
 133
 134 PG proda 4_TCOFFEE              PRODA
 135 PG proda type                   sequence_multiple_aligner
 136 PG proda ADDRESS                http://proda.stanford.edu
 137 PG proda language               C++
 138 PG proda language2              CXX
 139 PG proda source                 http://proda.stanford.edu/proda_1_0.tar.gz
 140 PG proda mode                   mcoffee
 141 PG proda version                1.0
 142
 143 PG fsa 4_TCOFFEE                FSA
 144 PG fsa type                     sequence_multiple_aligner
 145 PG fsa ADDRESS                  http://fsa.sourceforge.net/
 146 PG fsa language                 C++
 147 PG fsa language2                CXX
 148 PG fsa source                   http://sourceforge.net/projects/fsa/files/fsa-1.15.3.tar.gz/download/
 149 PG fsa mode                     mcoffee
 150 PG fsa version                  1.15.3
 151
 152 PG prank 4_TCOFFEE              PRANK
 153 PG prank type                   sequence_multiple_aligner
 154 PG prank ADDRESS                http://www.ebi.ac.uk/goldman-srv/prank/
 155 PG prank language               C++
 156 PG prank language2              CXX
 157 PG prank source                 http://www.ebi.ac.uk/goldman-srv/prank/src/prank/prank.src.100303.tgz
 158 PG prank mode                   mcoffee
 159 PG prank version                100303
 160
 161 PG sap 4_TCOFFEE                SAP
 162 PG sap type                     structure_pairwise_aligner
 163 PG sap ADDRESS                  http://mathbio.nimr.mrc.ac.uk/wiki/Software
 164 PG sap language                 C
 165 PG sap language2                C
 166 PG sap source                   http://mathbio.nimr.mrc.ac.uk/download/sap-1.1.1.tar.gz
 167 PG sap mode                     expresso,3dcoffee
 168 PG sap version                  1.1.1
 169
 170 PG TMalign 4_TCOFFEE            TMALIGN
 171 PG TMalign type                 structure_pairwise_aligner
 172 PG TMalign ADDRESS              http://zhang.bioinformatics.ku.edu/TM-align/TMalign.f
 173 PG TMalign language             Fortran
 174 PG TMalign language2            Fortran
 175 PG TMalign source               http://zhang.bioinformatics.ku.edu/TM-align/TMalign.f
 176 PG TMalign linux                http://zhang.bioinformatics.ku.edu/TM-align/TMalign_32.gz
 177 PG TMalign mode                 expresso,3dcoffee
 178 PG TMalign version              1.0
 179
 180
 181 PG mustang 4_TCOFFEE            MUSTANG
 182 PG mustang type                 structure_pairwise_aligner
 183 PG mustang ADDRESS              http://www.cs.mu.oz.au/~arun/mustang
 184 PG mustang language             C++
 185 PG mustang language2            CXX
 186 PG mustang source               http://ww2.cs.mu.oz.au/~arun/mustang/mustang_v3.2.1.tgz
 187 PG mustang mode                 expresso,3dcoffee
 188 PG mustang version              3.2.1
 189
 190 PG lsqman 4_TCOFFEE             LSQMAN
 191 PG lsqman type                  structure_pairwise_aligner
 192 PG lsqman ADDRESS               empty
 193 PG lsqman language              empty
 194 PG lsqman language2             empty
 195 PG lsqman source                empty
 196 PG lsqman update_action         never
 197 PG lsqman mode                  expresso,3dcoffee
 198
 199 PG align_pdb 4_TCOFFEE          ALIGN_PDB
 200 PG align_pdb type               structure_pairwise_aligner
 201 PG align_pdb ADDRESS            empty
 202 PG align_pdb language           empty
 203 PG align_pdb language2          empty
 204 PG align_pdb source             empty
 205 PG align_pdb update_action      never
 206 PG align_pdb mode               expresso,3dcoffee
 207
 208
 209 PG fugueali 4_TCOFFEE           FUGUE
 210 PG fugueali type                structure_pairwise_aligner
 211 PG fugueali ADDRESS             http://www-cryst.bioc.cam.ac.uk/fugue/download.html
 212 PG fugueali language            empty
 213 PG fugueali language2           empty
 214 PG fugueali source              empty
 215 PG fugueali update_action       never
 216 PG fugueali mode                expresso,3dcoffee
 217
 218 PG dalilite.pl 4_TCOFFEE        DALILITEc
 219 PG dalilite.pl type             structure_pairwise_aligner
 220 PG dalilite.pl ADDRESS          built_in
 221 PG dalilite.pl ADDRESS2         http://www.ebi.ac.uk/Tools/webservices/services/dalilite
 222 PG dalilite.pl language         Perl
 223 PG dalilite.pl language2        Perl
 224 PG dalilite.pl source           empty
 225 PG dalilite.pl update_action    never
 226 PG dalilite.pl mode             expresso,3dcoffee
 227
 228 PG probconsRNA 4_TCOFFEE        PROBCONSRNA
 229 PG probconsRNA type             RNA_multiple_aligner
 230 PG probconsRNA ADDRESS          http://probcons.stanford.edu/
 231 PG probconsRNA language         C++
 232 PG probconsRNA language2        CXX
 233 PG probconsRNA source           http://probcons.stanford.edu/probconsRNA.tar.gz
 234 PG probconsRNA mode             mcoffee,rcoffee
 235 PG probconsRNA version          1.0
 236
 237 PG sfold 4_TCOFFEE              CONSAN
 238 PG sfold type                   RNA_pairwise_aligner
 239 PG sfold ADDRESS                http://selab.janelia.org/software/consan/
 240 PG sfold language               empty
 241 PG sfold language2              empty
 242 PG sfold source                 empty
 243 PG sfold update_action          never
 244 PG sfold mode                   rcoffee
 245
 246 PG RNAplfold 4_TCOFFEE          RNAPLFOLD
 247 PG RNAplfold type               RNA_secondarystructure_predictor
 248 PG RNAplfold ADDRESS            http://www.tbi.univie.ac.at/~ivo/RNA/
 249 PG RNAplfold language           C
 250 PG RNAplfold language2          C
 251 PG RNAplfold source             http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-1.7.2.tar.gz
 252 PG RNAplfold mode               rcoffee, seq_reformat
 253 PG RNAplfold version            1.7.2
 254
 255 PG retree 4_TCOFFEE     PHYLIP
 256 PG retree type          RNA_secondarystructure_predictor
 257 PG retree ADDRESS       http://evolution.gs.washington.edu/phylip/
 258 PG retree language      C
 259 PG retree language2     C
 260 PG retree source        http://evolution.gs.washington.edu/phylip/download/phylip-3.69.tar.gz
 261 PG retree  mode         trmsd, seq_reformat
 262 PG retree  version      3.69
 263
 264
 265 PG hmmtop 4_TCOFFEE             HMMTOP
 266 PG hmmtop type                  protein_secondarystructure_predictor
 267 PG hmmtop ADDRESS               www.enzim.hu/hmmtop/
 268 PG hmmtop language              C
 269 PG hmmtop language2             C
 270 PG hmmtop source                empty
 271 PG hmmtop update_action         never
 272 PG hmmtop mode                  tcoffee
 273
 274 PG gorIV 4_TCOFFEE              GOR4
 275 PG gorIV type                   protein_secondarystructure_predictor
 276 PG gorIV ADDRESS                http://mig.jouy.inra.fr/logiciels/gorIV/
 277 PG gorIV language               C
 278 PG gorIV language2              C
 279 PG gorIV source                 http://mig.jouy.inra.fr/logiciels/gorIV/GOR_IV.tar.gz
 280 PG gorIV update_action          never
 281 PG gorIV mode                   tcoffee
 282
 283 PG wublast.pl 4_TCOFFEE         EBIWUBLASTc
 284 PG wublast.pl type              protein_homology_predictor
 285 PG wublast.pl ADDRESS           built_in
 286 PG wublast.pl ADDRESS2          http://www.ebi.ac.uk/Tools/webservices/services/wublast
 287 PG wublast.pl language          Perl
 288 PG wublast.pl language2         Perl
 289 PG wublast.pl source            empty
 290 PG wublast.pl update_action     never
 291 PG wublast.pl mode              psicoffee,expresso,accurate
 292
 293 PG blastpgp.pl 4_TCOFFEE        EBIBLASTPGPc
 294 PG blastpgp.pl type             protein_homology_predictor
 295 PG blastpgp.pl ADDRESS          built_in
 296 PG blastpgp.pl ADDRESS2         http://www.ebi.ac.uk/Tools/webservices/services/blastpgp
 297 PG blastpgp.pl language         Perl
 298 PG blastpgp.pl language2        Perl
 299 PG blastpgp.pl source           empty
 300 PG blastpgp.pl update_action    never
 301 PG blastpgp.pl mode             psicoffee,expresso,accurate
 302
 303
 304 PG blastcl3 4_TCOFFEE           NCBIWEBBLAST
 305 PG blastcl3 type                protein_homology_predictor
 306 PG blastcl3 ADDRESS             ftp://ftp.ncbi.nih.gov/blast/executables/LATEST
 307 PG blastcl3 language            C
 308 PG blastcl3 language2           C
 309 PG blastcl3 source              empty
 310 PG blastcl3 update_action       never
 311 PG blastcl3 mode                psicoffee,expresso,3dcoffee
 312
 313 PG blastall 4_TCOFFEE    blastall
 314 PG blastall type                 protein_homology_predictor
 315 PG blastall ADDRESS      ftp://ftp.ncbi.nih.gov/blast/executables/LATEST
 316 PG blastall language     C
 317 PG blastall language2    C
 318 PG blastall source       empty
 319 PG blastall update_action never
 320 PG blastall mode                 psicoffee,expresso,3dcoffee
 321
 322 PG legacy_blast.pl 4_TCOFFEE     NCBIBLAST
 323 PG legacy_blast.pl type          protein_homology_predictor
 324 PG legacy_blast.pl ADDRESS       ftp://ftp.ncbi.nih.gov/blast/executables/LATEST
 325 PG legacy_blast.pl language      C
 326 PG legacy_blast.pl language2     C
 327 PG legacy_blast.pl source        empty
 328 PG legacy_blast.pl update_action never
 329 PG legacy_blast.pl mode          psicoffee,expresso,3dcoffee
 330
 331 PG SOAP::Lite 4_TCOFFEE         SOAPLITE
 332 PG SOAP::Lite type              library
 333 PG SOAP::Lite ADDRESS           http://cpansearch.perl.org/src/MKUTTER/SOAP-Lite-0.710.08/Makefile.PL
 334 PG SOAP::Lite language          Perl
 335 PG SOAP::Lite language2         Perl
 336 PG SOAP::Lite source            empty
 337 PG blastpgp update_action       never
 338 PG SOAP::Lite mode              none
 339
 340 PG XML::Simple 4_TCOFFEE        XMLSIMPLE
 341 PG XML::Simple type             library
 342 PG XML::Simple ADDRESS          http://search.cpan.org/~grantm/XML-Simple-2.18/lib/XML/Simple.pm
 343 PG XML::Simple language         Perl
 344 PG XML::Simple language2        Perl
 345 PG XML::Simple source           empty
 346 PG XML::Simple mode             psicoffee,expresso,accurate
 347
 348
 349
 350 MODE tcoffee  name tcoffee
 351 MODE rcoffee  name rcoffee
 352 MODE 3dcoffee name 3dcoffee
 353 MODE mcoffee  name mcoffee
 354 MODE expresso name expresso
 355 MODE trmsd    name trmsd
 356 MODE accurate name accurate
 357 MODE seq_reformat name seq_reformat