Mercurial > repos > iuc > hyphy_slac

annotate test-data/gard-out1.json @ 33:365e33adf3a4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
author iuc
date Wed, 30 Mar 2022 00:15:09 +0000
parents 0c6724c345d9
children
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c2bed8cc8fc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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1 {
c2bed8cc8fc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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2 "analysis":{
c2bed8cc8fc1 "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",
c2bed8cc8fc1 "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",
c2bed8cc8fc1 "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",
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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,
0c6724c345d9 "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": [
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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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 },
c2bed8cc8fc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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18 "input":{
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19 "file name":"/tmp/tmpht3ax8lq/job_working_directory/000/2/working/./input.fasta",
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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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
c2bed8cc8fc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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23 },
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24 "potentialBreakpoints":21,
0c6724c345d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
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25 "singleTreeAICc":1450.968340686507,
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26 "siteBreakPointSupport":{
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27 "130":7.71938316947624e-08,
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28 "150":7.49872016582054e-06,
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29 "158":4.898720800158644e-06,
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30 "175":0.0001152764571690805,
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31 "176":0.000624401895637527,
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32 "183":8.845949780426112e-06,
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33 "196":5.17454230945286e-06,
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34 "197":5.9168232845333e-06,
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35 "198":4.436819044306368e-05,
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36 "227":2.830236103715775e-06,
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37 "233":9.74236872039044e-06,
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38 "241":1.802640814372882e-05,
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39 "245":1.305334911931824e-05,
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40 "252":8.580180939514955e-06,
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41 "253":2.317805781298633e-05,
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42 "260":1.77855732841814e-06,
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43 "287":4.449903505856628e-07,
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44 "325":6.636014843884652e-09,
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45 "326":2.134836027957093e-09,
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46 "334":7.302354343864046e-09,
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47 "341":1.678880851117679e-09,
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48 "358":6.863087158511391e-14
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c2bed8cc8fc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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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 }
c2bed8cc8fc1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
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55 }