Mercurial > repos > iuc > hyphy_absrel

annotate test-data/gard-out1.json @ 15:81e66674859e 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 adf0f20535bd585663c291f8f15137a7ba947949"
author iuc
date Fri, 21 Aug 2020 15:24:17 -0400
parents 5c87e4907e08
children 5f2ca10db92a
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5c87e4907e08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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1 {
5c87e4907e08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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2 "analysis":{
5c87e4907e08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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3 "authors":"Sergei L Kosakovsky Pond",
5c87e4907e08 "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",
5c87e4907e08 "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",
5c87e4907e08 "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.",
5c87e4907e08 "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.",
5c87e4907e08 "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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iuc
parents:
diff changeset
62 "number of sequences":21,
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iuc
parents:
diff changeset
63 "number of sites":1698,
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iuc
parents:
diff changeset
64 "partition count":1
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iuc
parents:
diff changeset
65 },
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iuc
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diff changeset
66 "potentialBreakpoints":244,
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diff changeset
67 "singleTreeAICc":8952.770360670584,
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parents:
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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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
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140 "1580":5.505818788734445e-49,
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iuc
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141 "1585":1.614020745294316e-49,
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iuc
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diff changeset
142 "159":2.814745521856487e-30,
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iuc
parents:
diff changeset
143 "161":5.278607654454491e-08,
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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
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iuc
parents:
diff changeset
157 "177":1.79882740520206e-07,
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iuc
parents:
diff changeset
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iuc
parents:
diff changeset
159 "180":3.648108711445327e-07,
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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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iuc
parents:
diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
parents:
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iuc
parents:
diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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parents:
diff changeset
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iuc
parents:
diff changeset
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diff changeset
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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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diff changeset
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iuc
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diff changeset
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iuc
parents:
diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
parents:
diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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iuc
parents:
diff changeset
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iuc
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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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iuc
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diff changeset
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iuc
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diff changeset
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iuc
parents:
diff changeset
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iuc
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diff changeset
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iuc
parents:
diff changeset
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iuc
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diff changeset
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iuc
parents:
diff changeset
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iuc
parents:
diff changeset
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iuc
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diff changeset
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iuc
parents:
diff changeset
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iuc
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diff changeset
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iuc
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diff changeset
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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
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iuc
parents:
diff changeset
212 "467":1.657561796358788e-05,
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iuc
parents:
diff changeset
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iuc
parents:
diff changeset
214 "498":1.148320825350936e-24,
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iuc
parents:
diff changeset
215 "50":8.32428744865e-23,
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iuc
parents:
diff changeset
216 "509":1.189408841111924e-08,
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iuc
parents:
diff changeset
217 "511":2.022119078897978e-24,
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iuc
parents:
diff changeset
218 "513":3.201599896136264e-07,
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iuc
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diff changeset
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iuc
parents:
diff changeset
220 "522":2.646016563727863e-07,
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iuc
parents:
diff changeset
221 "524":2.999275395428511e-07,
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iuc
parents:
diff changeset
222 "531":7.048583824652365e-06,
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iuc
parents:
diff changeset
223 "532":8.871326441721272e-07,
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iuc
parents:
diff changeset
224 "534":0.008873756999646102,
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iuc
parents:
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301 },
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5c87e4907e08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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5c87e4907e08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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5c87e4907e08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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5c87e4907e08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
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5c87e4907e08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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5c87e4907e08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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5c87e4907e08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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5c87e4907e08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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5c87e4907e08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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318 }