Mercurial > repos > iuc > hyphy_prime

annotate test-data/gard-out1.json @ 14:02f0dfb10421 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 05ae58b803965f16da05329ef4a84fa6434382ce"
author iuc
date Fri, 09 Apr 2021 21:51:27 +0000
parents 725ef5f6d749
children 6d29207a32c5
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725ef5f6d749 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
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1 {
725ef5f6d749 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
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2 "analysis":{
725ef5f6d749 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
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3 "authors":"Sergei L Kosakovsky Pond",
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4 "citation":"**Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm**, _Mol Biol Evol 23(10), 1891–1901",
725ef5f6d749 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
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5 "contact":"spond@temple.edu",
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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.",
725ef5f6d749 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
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7 "requirements":"A sequence alignment.",
725ef5f6d749 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
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8 "version":"0.1"
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9 },
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10 "baselineScore":8884.998566352424,
725ef5f6d749 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
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11 "breakpointData":{
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12 "0":{
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35 }
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37 "improvements":{
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42 "deltaAICc":121.2176698921212
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60 "input":{
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61 "file name":"/Users/ryanvelazquez/Documents/galaxy_items/tools-iuc/tools/hyphy/./test-data/gard-in1.fa",
725ef5f6d749 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
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62 "number of sequences":21,
725ef5f6d749 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
iuc
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diff changeset
63 "number of sites":1698,
725ef5f6d749 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
iuc
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diff changeset
64 "partition count":1
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iuc
parents:
diff changeset
65 },
725ef5f6d749 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
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diff changeset
66 "potentialBreakpoints":244,
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iuc
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diff changeset
67 "singleTreeAICc":8952.770360670584,
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iuc
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diff changeset
68 "siteBreakPointSupport":{
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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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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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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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iuc
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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
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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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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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105 "134":7.744769428033727e-17,
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iuc
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106 "1361":2.822486839844269e-33,
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iuc
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iuc
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iuc
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109 "1412":6.831611952947673e-38,
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iuc
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110 "1418":1.522690852126543e-39,
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iuc
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111 "1430":7.96352395927298e-40,
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iuc
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iuc
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iuc
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114 "144":8.552230281908163e-07,
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iuc
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115 "1442":2.016530452321108e-37,
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iuc
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116 "1454":2.386567702095966e-36,
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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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121 "149":1.304259029589306e-05,
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iuc
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iuc
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iuc
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iuc
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125 "151":1.790975065283929e-08,
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iuc
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126 "1515":4.749012537570416e-45,
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iuc
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127 "1516":1.058313486583168e-45,
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iuc
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128 "1519":3.729412022561233e-46,
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iuc
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iuc
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iuc
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133 "1526":3.855324589536673e-46,
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iuc
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iuc
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135 "1538":3.417841619348906e-47,
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iuc
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iuc
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137 "1544":1.7639941893744e-47,
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iuc
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138 "155":1.315748190900565e-29,
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iuc
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139 "1556":1.89572005098281e-47,
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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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142 "159":2.814745521856487e-30,
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iuc
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143 "161":5.278607654454491e-08,
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iuc
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144 "1610":6.983674612335563e-50,
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iuc
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diff changeset
145 "1613":1.219959907173526e-49,
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iuc
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diff changeset
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725ef5f6d749 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
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725ef5f6d749 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
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311 "2":{
725ef5f6d749 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
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725ef5f6d749 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
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725ef5f6d749 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
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725ef5f6d749 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
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725ef5f6d749 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
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725ef5f6d749 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
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317 }
725ef5f6d749 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
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318 }