Mercurial > repos > iuc > hyphy_sm19
diff test-data/summary/nsp7.SLAC.json @ 26:af92956bfe88 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
author | iuc |
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date | Wed, 09 Jun 2021 07:05:34 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp7.SLAC.json Wed Jun 09 07:05:34 2021 +0000 @@ -0,0 +1,5244 @@ +{ + "MLE":{ + "content":{ + "0":{ + "by-branch":{ + "AVERAGED": [ +[75.21726851651356, 163.6940894156486, 0, 1, 0.3148333723751685, 0, 0.006108956062920642, 0.007567306802312253, 0.6851666276248315, 1, 0.004137678108204586], + [0, 0, 0, 0, null, null, null, null, 1, 1, 0], + [75.2497273928074, 163.6616305393547, 1, 0, 0.3149692339623897, 0.0132890846870441, 0, -0.01646150011769675, 1, 0.3149692339623897, 0.00413937051268764], + [0, 0, 0, 0, null, null, null, null, 1, 1, 0], + [75.28831762809149, 163.6291716630609, 0, 1, 0.3151226720633364, 0, 0.006111379712042806, 0.00757030903318438, 0.6848773279366636, 1, 0.004130319073497585], + [74.98180835674931, 163.9394365862927, 0, 1, 0.3138348302790098, 0, 0.006099813570321934, 0.007555981782829428, 0.6861651697209902, 1, 0.004133581103629891], + [75.20828178574392, 163.7092075054085, 1, 0, 0.3147876784109879, 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probability that S is no less than the observed value, with P<sub>s</sub> probability of success"], + ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"] + ] + }, + "analysis":{ + "authors":"Sergei L Kosakovsky Pond and Simon DW Frost", + "citation":"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222", + "contact":"spond@temple.edu", + "info":"SLAC (Single Likelihood Ancestor Counting)\n uses a maximum likelihood ancestral state reconstruction\n and minimum path substitution counting to estimate site - level\n dS and dN,\n and applies a simple binomial - based test to test\n if dS differs drom dN.\n The estimates aggregate information over all branches,\n so the signal is derived from\n pervasive diversification or conservation. A subset of branches can be selected\n for testing as well.\n Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ", + "requirements":"in-frame codon alignment and a phylogenetic tree", + "version":"2.00" + }, + "branch attributes":{ + "0":{ + "Node126":{ + "Global MG94xREV":0.004136417827218518, + "Nucleotide GTR":0.004026916786386125, + "amino-acid": [ +["S", "K", "M", "S", "D", "V", "K", "C", "T", "S", "V", "V", "L", "L", "S", "V", "L", "Q", "Q", "L", "R", "V", "E", "S", "S", "S", "K", "L", "W", "A", "Q", "C", "V", "Q", "L", "H", "N", "D", "I", "L", "L", "A", "K", "D", "T", "T", "E", "A", "F", "E", "K", "M", "V", "S", "L", "L", "S", "V", "L", "L", "S", "M", "Q", "C", "A", "V", "D", "I", "N", "K", "L", "C", "E", "E", "M", "L", "D", "N", "R", "A", "T", "L", "Q"] + ], + "codon": [ +["TCT", "AAA", "ATG", "TCA", "GAT", "GTA", "AAG", "TGC", "ACA", "TCA", "GTA", "GTC", "TTA", "CTC", "TCA", "GTT", "TTG", "CAA", "CAA", "CTC", "AGA", "GTA", 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GTR":{ + "AIC-c":4207.652962845961, + "Equilibrium frequencies": [ +[0.316982214572576], + [0.1955372510449963], + [0.1847799360708139], + [0.3027005983116138] + ], + "Log Likelihood":-1703.562299296798, + "Rate Distributions":{ + "Substitution rate from nucleotide A to nucleotide C":0.2854468704485844, + "Substitution rate from nucleotide A to nucleotide G":1, + "Substitution rate from nucleotide A to nucleotide T":0.009867778509707405, + "Substitution rate from nucleotide C to nucleotide G":0.02709890342210576, + "Substitution rate from nucleotide C to nucleotide T":1.655264438379606, + "Substitution rate from nucleotide G to nucleotide T":0.4850813979618184 + }, + "display order":0, + "estimated parameters":397 + } + }, + "input":{ + "file name":"/home/aglucaci/SARS-CoV-2/clades/B-1-617/nsp7.combined.fas", + "number of sequences":196, + "number of sites":83, + "partition count":1, + "trees":{ + 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