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
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
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
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
48 PG poa type sequence_multiple_aligner
49 PG poa ADDRESS http://www.bioinformatics.ucla.edu/poa/
52 PG poa source http://downloads.sourceforge.net/poamsa/poaV2.tar.gz
53 PG poa DIR /usr/share/
54 PG poa FILE1 blosum80.mat
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
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/
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
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
88 PG pcma 4_TCOFFEE PCMA
89 PG pcma type sequence_multiple_aligner
90 PG pcma ADDRESS ftp://iole.swmed.edu/pub/PCMA/
93 PG pcma source ftp://iole.swmed.edu/pub/PCMA/pcma.tar.gz
96 PG kalign 4_TCOFFEE KALIGN
97 PG kalign type sequence_multiple_aligner
98 PG kalign ADDRESS http://msa.cgb.ki.se
100 PG kalign language2 C
101 PG kalign source http://msa.cgb.ki.se/downloads/kalign/current.tar.gz
102 PG kalign mode mcoffee
105 PG amap 4_TCOFFEE AMAP
106 PG amap type sequence_multiple_aligner
107 PG amap ADDRESS http://bio.math.berkeley.edu/amap/
109 PG amap language2 CXX
110 PG amap source http://baboon.math.berkeley.edu/amap/download/amap.2.2.tar.gz
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
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
131 PG sap type structure_pairwise_aligner
132 PG sap ADDRESS http://mathbio.nimr.mrc.ac.uk/wiki/Software
135 PG sap source http://www.tcoffee.org/Packages/sap_distribution_TCC_0.6.tar.gz
136 PG sap mode expresso,3dcoffee
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
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
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
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
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
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
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
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
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
219 PG hmmtop 4_TCOFFEE HMMTOP
220 PG hmmtop type protein_secondarystructure_predictor
221 PG hmmtop ADDRESS www.enzim.hu/hmmtop/
223 PG hmmtop language2 C
224 PG hmmtop source empty
225 PG hmmtop update_action never
226 PG hmmtop mode tcoffee
228 PG gorIV 4_TCOFFEE GOR4
229 PG gorIV type protein_secondarystructure_predictor
230 PG gorIV ADDRESS http://mig.jouy.inra.fr/logiciels/gorIV/
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
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
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
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
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
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
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