Mercurial > repos > iuc > hyphy_strike_ambigs

annotate test-data/gard-out1.json @ 2:4bf743518e41 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
author iuc
date Tue, 27 Apr 2021 18:00:33 +0000
parents 7c86ceaf523c
children
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1 {
7c86ceaf523c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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2 "analysis":{
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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",
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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. v0.2 adds and spooling results to JSON after each breakpoint search conclusion",
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7 "requirements":"A sequence alignment.",
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8 "version":"0.2"
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9 },
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10 "baselineScore":1450.968340148184,
4bf743518e41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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11 "bestModelAICc":1450.968340148184,
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12 "breakpointData":{
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13 "bps": [
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14 [1, 428]
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15 ],
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16 "tree":"((BRO1_1:0,BRO2:0.007408926175080497)Node1:0,(BRO3_1:0.002455524404855022,BRO4:0.002457415365886074)Node4:0,(((BRO5:0.002464479112430666,(BRO6:0.004940850926103086,BRO7_1:0)Node11:0)Node9:0.002460542727794925,(BRO9:0.004931390913247289,((BRO10:0.002933649980980302,BRO11_1:0.01453409151831228)Node17:0.002436921831192641,BRO12:0.006987081661112447)Node16:0.005417113782285573)Node14:0)Node8:0,BRO8:0.002462026756884335)Node7:0)"
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17 },
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18 "input":{
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19 "file name":"/tmp/tmpht3ax8lq/job_working_directory/000/2/working/./input.fasta",
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20 "number of sequences":12,
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21 "number of sites":428,
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22 "partition count":1
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23 },
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24 "potentialBreakpoints":21,
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25 "singleTreeAICc":1450.968340686507,
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26 "siteBreakPointSupport":{
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48 "358":6.863087158511391e-14
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49 },
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50 "timeElapsed":8,
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51 "totalModelCount":209,
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52 "trees":{
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53 "newickString":"((BRO1_1:0,BRO2:0.007408926175080497)Node1:0,(BRO3_1:0.002455524404855022,BRO4:0.002457415365886074)Node4:0,(((BRO5:0.002464479112430666,(BRO6:0.004940850926103086,BRO7_1:0)Node11:0)Node9:0.002460542727794925,(BRO9:0.004931390913247289,((BRO10:0.002933649980980302,BRO11_1:0.01453409151831228)Node17:0.002436921831192641,BRO12:0.006987081661112447)Node16:0.005417113782285573)Node14:0)Node8:0,BRO8:0.002462026756884335)Node7:0)"
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54 }
7c86ceaf523c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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55 }