Mercurial > repos > iuc > hyphy_fubar

annotate test-data/gard-out1.json @ 10:73833ae53fbb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8abccd4b7a288b6a321a6662eec88577ad83b36f"
author iuc
date Wed, 22 Apr 2020 12:11:07 -0400
parents 0f108ee932ea
children cd41e7a4d35f
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0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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1 {
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2 "analysis":{
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3 "authors":"Sergei L Kosakovsky Pond",
0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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4 "citation":"**Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm**, _Mol Biol Evol 23(10), 1891–1901",
0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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5 "contact":"spond@temple.edu",
0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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6 "info":"GARD : Genetic Algorithms for Recombination Detection. Implements a heuristic\n approach to screening alignments of sequences for recombination, by using the CHC genetic algorithm to search for phylogenetic\n incongruence among different partitions of the data. The number of partitions is determined using a step-up procedure, while the\n placement of breakpoints is searched for with the GA. The best fitting model (based on c-AIC) is returned; and additional post-hoc\n tests run to distinguish topological incongruence from rate-variation.",
0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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7 "requirements":"A sequence alignment.",
0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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8 "version":"0.1"
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9 },
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10 "baselineScore":8884.998566352424,
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11 "breakpointData":{
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61 "file name":"/Users/ryanvelazquez/Documents/galaxy_items/tools-iuc/tools/hyphy/./test-data/gard-in1.fa",
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diff changeset
62 "number of sequences":21,
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diff changeset
63 "number of sites":1698,
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diff changeset
64 "partition count":1
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parents:
diff changeset
65 },
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diff changeset
66 "potentialBreakpoints":244,
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diff changeset
67 "singleTreeAICc":8952.770360670584,
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diff changeset
68 "siteBreakPointSupport":{
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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diff changeset
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iuc
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iuc
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diff changeset
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diff changeset
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iuc
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iuc
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iuc
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iuc
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iuc
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iuc
parents:
diff changeset
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iuc
parents:
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iuc
parents:
diff changeset
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iuc
parents:
diff changeset
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iuc
parents:
diff changeset
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iuc
parents:
diff changeset
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0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
144 "1610":6.983674612335563e-50,
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iuc
parents:
diff changeset
145 "1613":1.219959907173526e-49,
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iuc
parents:
diff changeset
146 "1616":1.379005387331829e-49,
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iuc
parents:
diff changeset
147 "1618":1.403866743396411e-51,
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iuc
parents:
diff changeset
148 "1619":6.05913881499244e-52,
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iuc
parents:
diff changeset
149 "1631":1.563107434100785e-52,
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iuc
parents:
diff changeset
150 "1632":5.045949522041951e-52,
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iuc
parents:
diff changeset
151 "1644":1.457045566204417e-52,
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iuc
parents:
diff changeset
152 "1646":1.817307863422175e-52,
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iuc
parents:
diff changeset
153 "1658":2.336582715408929e-53,
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iuc
parents:
diff changeset
154 "173":3.057688318766887e-09,
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iuc
parents:
diff changeset
155 "174":3.878560193985558e-09,
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iuc
parents:
diff changeset
156 "176":8.37052095471109e-08,
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iuc
parents:
diff changeset
157 "177":1.79882740520206e-07,
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iuc
parents:
diff changeset
158 "178":4.189275930585918e-07,
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iuc
parents:
diff changeset
159 "180":3.648108711445327e-07,
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iuc
parents:
diff changeset
160 "185":8.602578155282706e-07,
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iuc
parents:
diff changeset
161 "191":2.146033440200939e-05,
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iuc
parents:
diff changeset
162 "197":1.254742955877914e-07,
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iuc
parents:
diff changeset
163 "203":1.782085063210574e-09,
0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
164 "205":3.9041258553037e-08,
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iuc
parents:
diff changeset
165 "206":6.68882932678853e-21,
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iuc
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diff changeset
166 "209":6.086107365200133e-07,
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iuc
parents:
diff changeset
167 "218":3.339578115382376e-06,
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iuc
parents:
diff changeset
168 "230":4.417475117693213e-07,
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iuc
parents:
diff changeset
169 "233":5.355261458449197e-05,
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iuc
parents:
diff changeset
170 "236":0.007922604577960988,
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iuc
parents:
diff changeset
171 "239":0.001674452816751232,
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iuc
parents:
diff changeset
172 "242":0.003084865524315277,
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iuc
parents:
diff changeset
173 "251":0.001911517032820398,
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iuc
parents:
diff changeset
174 "257":0.001206425464437376,
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iuc
parents:
diff changeset
175 "266":0.0006256067585931275,
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iuc
parents:
diff changeset
176 "272":0.0004205386287599137,
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iuc
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diff changeset
177 "295":0.0006020604873750697,
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iuc
parents:
diff changeset
178 "298":7.88207661427839e-10,
0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
179 "303":1.196432870877656e-11,
0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
180 "304":4.034129303399593e-10,
0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
181 "310":1.00120863585874e-18,
0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
182 "320":9.255079503229926e-08,
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iuc
parents:
diff changeset
183 "326":1.316695923941227e-11,
0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
184 "327":9.749462853855344e-30,
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iuc
parents:
diff changeset
185 "328":5.468914334726157e-06,
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iuc
parents:
diff changeset
186 "335":5.399829244004923e-09,
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iuc
parents:
diff changeset
187 "336":1.259324706217958e-11,
0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
188 "338":4.933684745749596e-07,
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iuc
parents:
diff changeset
189 "348":4.415481383174255e-09,
0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
190 "383":1.208370214471027e-18,
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iuc
parents:
diff changeset
191 "391":4.182822911348255e-18,
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iuc
parents:
diff changeset
192 "407":6.023041146737167e-09,
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iuc
parents:
diff changeset
193 "414":5.844791249373782e-06,
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iuc
parents:
diff changeset
194 "417":1.35252270798266e-09,
0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
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iuc
parents:
diff changeset
196 "419":2.325837885934838e-10,
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iuc
parents:
diff changeset
197 "424":1.929854665115397e-05,
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iuc
parents:
diff changeset
198 "425":8.20012614644675e-05,
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iuc
parents:
diff changeset
199 "426":4.822853182787663e-05,
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iuc
parents:
diff changeset
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iuc
parents:
diff changeset
201 "437":3.538850116792625e-27,
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iuc
parents:
diff changeset
202 "440":0.08010977685280053,
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iuc
parents:
diff changeset
203 "448":0.07606312788914485,
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iuc
parents:
diff changeset
204 "45":5.811735655101648e-16,
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iuc
parents:
diff changeset
205 "453":0.03671194147765044,
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iuc
parents:
diff changeset
206 "455":0.02091509793683489,
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iuc
parents:
diff changeset
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iuc
parents:
diff changeset
208 "460":0.7998321443046799,
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iuc
parents:
diff changeset
209 "461":1,
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iuc
parents:
diff changeset
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iuc
parents:
diff changeset
211 "466":0.0008356143264203861,
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iuc
parents:
diff changeset
212 "467":1.657561796358788e-05,
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iuc
parents:
diff changeset
213 "468":1.348444812921266e-23,
0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
214 "498":1.148320825350936e-24,
0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
215 "50":8.32428744865e-23,
0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
216 "509":1.189408841111924e-08,
0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
217 "511":2.022119078897978e-24,
0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
218 "513":3.201599896136264e-07,
0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
219 "518":2.988923843741992e-13,
0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
220 "522":2.646016563727863e-07,
0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
221 "524":2.999275395428511e-07,
0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
222 "531":7.048583824652365e-06,
0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
223 "532":8.871326441721272e-07,
0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
224 "534":0.008873756999646102,
0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
225 "535":0.004214591771216962,
0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
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parents:
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iuc
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iuc
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iuc
parents:
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parents:
diff changeset
301 },
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diff changeset
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parents:
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304 "trees":{
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305 "0":{
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0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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0f108ee932ea "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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