1 PG t_coffee 4_TCOFFEE TCOFFEE
2 PG t_coffee type sequence_multiple_aligner
3 PG t_coffee ADDRESS http://www.tcoffee.org
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
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
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
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
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
52 PG poa type sequence_multiple_aligner
53 PG poa ADDRESS http://www.bioinformatics.ucla.edu/poa/
56 PG poa source http://downloads.sourceforge.net/poamsa/poaV2.tar.gz
57 PG poa DIR /usr/share/
58 PG poa FILE1 blosum80.mat
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
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/
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
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
95 PG mus4 4_TCOFFEE MUS4
96 PG mus4 type sequence_multiple_aligner
97 PG mus4 ADDRESS http://www.drive5.com/muscle/
100 PG mus4 source http://www.drive5.com/muscle/muscle4.0_src.tar.gz
101 PG mus4 mode mcoffee,rcoffee
105 PG pcma 4_TCOFFEE PCMA
106 PG pcma type sequence_multiple_aligner
107 PG pcma ADDRESS ftp://iole.swmed.edu/pub/PCMA/
110 PG pcma source ftp://iole.swmed.edu/pub/PCMA/pcma.tar.gz
114 PG kalign 4_TCOFFEE KALIGN
115 PG kalign type sequence_multiple_aligner
116 PG kalign ADDRESS http://msa.cgb.ki.se
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
124 PG amap 4_TCOFFEE AMAP
125 PG amap type sequence_multiple_aligner
126 PG amap ADDRESS http://bio.math.berkeley.edu/amap/
128 PG amap language2 CXX
129 PG amap source http://amap-align.googlecode.com/files/amap.2.0.tar.gz
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
144 PG fsa type sequence_multiple_aligner
145 PG fsa ADDRESS http://fsa.sourceforge.net/
148 PG fsa source http://sourceforge.net/projects/fsa/files/fsa-1.15.3.tar.gz/download/
150 PG fsa version 1.15.3
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
162 PG sap type structure_pairwise_aligner
163 PG sap ADDRESS http://mathbio.nimr.mrc.ac.uk/wiki/Software
166 PG sap source http://mathbio.nimr.mrc.ac.uk/download/sap-1.1.1.tar.gz
167 PG sap mode expresso,3dcoffee
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
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
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
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
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
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
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
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
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
255 PG retree 4_TCOFFEE PHYLIP
256 PG retree type RNA_secondarystructure_predictor
257 PG retree ADDRESS http://evolution.gs.washington.edu/phylip/
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
265 PG hmmtop 4_TCOFFEE HMMTOP
266 PG hmmtop type protein_secondarystructure_predictor
267 PG hmmtop ADDRESS www.enzim.hu/hmmtop/
269 PG hmmtop language2 C
270 PG hmmtop source empty
271 PG hmmtop update_action never
272 PG hmmtop mode tcoffee
274 PG gorIV 4_TCOFFEE GOR4
275 PG gorIV type protein_secondarystructure_predictor
276 PG gorIV ADDRESS http://mig.jouy.inra.fr/logiciels/gorIV/
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
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
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
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
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
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
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
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
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