Mercurial > repos > iuc > hyphy_cfel
diff test-data/summary/nsp8.FEL.json @ 3:c046f72e5e3a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
| author | iuc |
|---|---|
| date | Wed, 09 Jun 2021 06:58:21 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.FEL.json Wed Jun 09 06:58:21 2021 +0000 @@ -0,0 +1,581 @@ +{ + "MLE":{ + "content":{ + "0": [ +[0, 0, 0, 0, 1, 0], + [0, 0, 0, 0, 1, 0], + [3.195197959507056, 0, 3.205811877302111, 0.002772105520872259, 0.9580101497567953, 0], + [0, 0, 0, 0, 1, 0], + [0, 0, 0, -7.296727429917382e-05, 1, 0], + [0, 0, 0, 0, 1, 0], + [0, 0, 0, 0, 1, 0], + [3.238107125504523, 0, 3.213547473340999, 0.003030822331904659, 0.9560963156973498, 0], + [0, 1.332038499257686, 0, -0.001332719656321757, 1, 0], + [0, 0, 0, 0, 1, 0], + [0, 0, 0, 0, 1, 0], + [0, 0, 0, 0, 1, 0], + [0, 0, 0, 0, 1, 0], + [6.598685982136248, 0.2251722656465092, 6.592228961936009, 0.005547079257077314, 0.9406294756580599, 0], + [0, 0, 0, -2.674095220811523e-06, 1, 0], + [6.598685982136248, 0.2251722656465092, 6.592228961936009, 0.005547079257077314, 0.9406294756580599, 0], + [0, 0, 0, 0, 1, 0], + [6.158743797064303, 0.2592752451004765, 6.174124078617361, 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Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222", + "contact":"spond@temple.edu", + "info":"FEL (Fixed Effects Likelihood)\n estimates site-wise synonymous (α) and non-synonymous (β) rates, and\n uses a likelihood ratio test to determine if beta &neq; alpha at a site.\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, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing.\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":"2.1" + }, + "branch attributes":{ + "0":{ + "Node20":{ + "Global MG94xREV":0.001634412620939209, + "Nucleotide GTR":0.001684521619549293 + }, + "Node38":{ + "Global MG94xREV":0.001735516186079463, + "Nucleotide GTR":0.00168484920326581 + }, + "Node4":{ + "Global MG94xREV":0.001634082124264937, + "Nucleotide GTR":0.001683801387489096 + }, + "REFERENCE":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"REFERENCE" + }, + "epi_isl_1181694_hCoV_19_USA_DE_DHSS_B1064373_2021":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"epi_isl_1181694/hCoV-19/USA/DE-DHSS-B1064373/2021" + }, + "epi_isl_1357692_hCoV_19_India_WB_1931500870015_2021":{ + "Global MG94xREV":0.001732287231356377, + "Nucleotide GTR":0.001682745450340891, + "original name":"epi_isl_1357692/hCoV-19/India/WB-1931500870015/2021" + }, + "epi_isl_1384851_hCoV_19_India_MH_NCCS_ND13683_2021":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"epi_isl_1384851/hCoV-19/India/MH-NCCS-ND13683/2021" + }, + "epi_isl_1415270_hCoV_19_India_MH_NCCS_BJ2_2021":{ + "Global MG94xREV":0.001731614563238503, + "Nucleotide GTR":0.00168274558227101, + "original name":"epi_isl_1415270/hCoV-19/India/MH-NCCS-BJ2/2021" + }, + "epi_isl_1416968_hCoV_19_Guadeloupe_IPP06229_2021":{ + "Global MG94xREV":0.001735723694712937, + "Nucleotide GTR":0.001684401404203384, + "original name":"epi_isl_1416968/hCoV-19/Guadeloupe/IPP06229/2021" + }, + "epi_isl_1533793_hCoV_19_India_MH_NCCS_CHN21027888_2021":{ + "Global MG94xREV":0.001732400229866267, + "Nucleotide GTR":0.00168406792173386, + "original 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+ } + } +} \ No newline at end of file