Mercurial > repos > iuc > hyphy_summary
diff test-data/summary/nsp8.CFEL.json @ 0:f304c108aa1f draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
| author | iuc |
|---|---|
| date | Wed, 09 Jun 2021 07:03:54 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.CFEL.json Wed Jun 09 07:03:54 2021 +0000 @@ -0,0 +1,589 @@ +{ + "MLE":{ + "content":{ + "0": [ +[0, 0, 0, 0, 1, 1, 1, 1, 1, 0], + [0, 0, 0, 0, 1, 1, 1, 1, 1, 0], + [3.206171473304911, 0, 0.03175555207671071, 5.433962997865532e-05, 0, 0, 0.9766417072604165, 1, -1, 0.1428350861439815], + [0, 0, 0, 0, 1, 1, 1, 1, 1, 0], + [0, 2.691597641547223, 0.6095939176926283, 0, 0, 0, 1, 1, -1, 0.334509864610243], + [0, 0, 0, 0, 1, 1, 1, 1, 1, 0], + [0, 0, 0, 0, 1, 1, 1, 1, 1, 0], + [3.229642435228862, 0, 2.162021710309243, 0.004452160407161729, 0, 0, 0.8693548005974709, 1, -1, 0.1442288861347906], + [0, 2.170494633509469, 0.2961869984298745, 0, 0, 0, 0.9875062279782896, 1, -1, 0.2697178710749373], + [0, 0, 0, 0, 1, 1, 1, 1, 1, 0], + [0, 0, 0, 0, 1, 1, 1, 1, 1, 0], + [0, 0, 0, 0, 1, 1, 1, 1, 1, 0], + [0, 0, 0, 0, 1, 1, 1, 1, 1, 0], + [6.636646908481298, 0, 1.139449512908137, 6.624437421595782e-05, 0, 0, 0.906603671841744, 1, 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"Q-value for the test that non-synonymous rates differ between any of the selected groups: B-1-617,Reference"], + ["Permutation p-value", "Label permutation test for significant sites"], + ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale beta-alpha"] + ] + }, + "analysis":{ + "authors":"Sergei L Kosakovsky Pond and Steven Weaver", + "citation":"TBD", + "contact":"spond@temple.edu", + "help":"http://www.hyphy.org/methods/other/contrast-fel/", + "info":"Contrast-FEL (Fixed Effects Likelihood) investigates whether or not selective pressures differ between two or more sets of\n branches at a site. Site-specific synonymous (alpha) and non-synonymous (beta, one per branch set) substitution rates are estimated\n and then beta rates are tested for equality at each site. LRT and permutation tests ar used to assess significance at each site, and FDR is applied alignment wide to call sites with different selective profiles", + "requirements":"in-frame codon alignment and a phylogenetic tree; only single partition data are supported", + "version":"0.5" + }, + "branch attributes":{ + "0":{ + "Node20":{ + "Global MG94xREV":0.001634892186392535, + "Nucleotide GTR":0.001684521619549293 + }, + "Node38":{ + "Global MG94xREV":0.001919664151147453, + "Nucleotide GTR":0.00168484920326581 + }, + "Node4":{ + "Global MG94xREV":0.001634608725470079, + "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":0.001728428286527107, + "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":0.001727412680411063, + "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":0.001731169192232254, + "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":0.001728394297110263, + "Nucleotide GTR":0.00168406792173386, + "original name":"epi_isl_1533793/hCoV-19/India/MH-NCCS-CHN21027888/2021" + }, + "epi_isl_1543980_hCoV_19_Singapore_490_2021":{ + "Global MG94xREV":0.001731480337658913, + "Nucleotide GTR":0.001684975469042935, + "original name":"epi_isl_1543980/hCoV-19/Singapore/490/2021" + }, + "epi_isl_1544068_hCoV_19_India_MH_NCCS_RT231527_2021":{ + "Global MG94xREV":0.00173257034392943, + "Nucleotide GTR":0.001684401583391051, + "original name":"epi_isl_1544068/hCoV-19/India/MH-NCCS-RT231527/2021" + }, + "epi_isl_1573247_hCoV_19_Germany_un_RKI_I_068985_2021":{ + "Global MG94xREV":0.001728428527066194, + "Nucleotide GTR":0.001682745512695379, + "original name":"epi_isl_1573247/hCoV-19/Germany/un-RKI-I-068985/2021" + }, + "epi_isl_1589870_hCoV_19_India_WB_1931501009078_2021":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"epi_isl_1589870/hCoV-19/India/WB-1931501009078/2021" + }, + "epi_isl_1589885_hCoV_19_India_WB_1931300250528_2021":{ + "Global MG94xREV":0.001730278969738805, + "Nucleotide GTR":0.001684431017860219, + "original name":"epi_isl_1589885/hCoV-19/India/WB-1931300250528/2021" + }, + 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109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197] + ], + "name":"fel.filter.default" + } + }, + "fits":{ + "Global MG94xREV":{ + "AIC-c":2512.992528252278, + "Equilibrium frequencies": [ +[0.03825952761243274], + [0.01370948533169502], + [0.0238326285579188], + [0.05169206288834598], + [0.02910782227384961], + [0.01043016700423795], + [0.01813184740308045], + [0.03932728586627101], + [0.01035067712195123], + [0.003708944282165923], + [0.006447644771501305], + [0.01398469573761802], + [0.0283653688047424], + [0.01016412464618009], + [0.01766935821790241], + [0.03832416445281453], + 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C to nucleotide G":1.129990583516242, + "Substitution rate from nucleotide C to nucleotide T":2.723444388603395, + "Substitution rate from nucleotide G to nucleotide T":1.720896006888861 + }, + "display order":0, + "estimated parameters":69 + } + }, + "input":{ + "file name":"/home/aglucaci/SARS-CoV-2/clades/B-1-617/nsp8.combined.fas", + "number of sequences":32, + "number of sites":198, + "partition count":1, + "trees":{ + 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