Mercurial > repos > iuc > hyphy_absrel
diff test-data/summary/nsp8.PRIME.json @ 27:8633ea985719 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 00684bab4c9e740cfa6a39abc444380e6818fd97"
| author | iuc |
|---|---|
| date | Wed, 09 Jun 2021 07:04:45 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary/nsp8.PRIME.json Wed Jun 09 07:04:45 2021 +0000 @@ -0,0 +1,596 @@ +{ + "MLE":{ + "content":{ + "0": [ +[0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0], + [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0], + [3.250710398632764, 2.543979863949704, 0.000260278000831112, -9.279879778998792, -9.280586210458985, 1, -0.03083220306091588, 1, -9.279441534952744, 0.246012012715961, 1, -9.279441534952742, 0.3671614662852546, 1, -9.279441534952742, -0.1712639841078613, 1, -9.279441534952737, 0.2624930750589453, 1, -9.279441534952737], + [0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0], + [0, 0.5537159057721711, 1.458738094193731e-05, -9.653318580984834, -9.653547984340634, 1, 0.5104924519363182, 1, -9.653308651005229, -0.1367278481442925, 1, -9.653308651005229, 0.5919809397222774, 1, -9.653308651005229, -0.1178049485056483, 1, -9.653308651005229, 0.6168893659032167, 1, 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Factor II secondary structure"], + ["λ3", "Importance for Factor III volume"], + ["p3", "p-value for non-zero effect of Factor III volume"], + ["LogL3", "Log likelihood when there is no effect of Factor III volume"], + ["λ4", "Importance for Factor IV composition"], + ["p4", "p-value for non-zero effect of Factor IV composition"], + ["LogL4", "Log likelihood when there is no effect of Factor IV composition"], + ["λ5", "Importance for Factor V charge"], + ["p5", "p-value for non-zero effect of Factor V charge"], + ["LogL5", "Log likelihood when there is no effect of Factor V charge"] + ] + }, + "analysis":{ + "authors":"Sergei L. Kosakovsky Pond", + "citation":"TBD", + "contact":"spond@temple.edu", + "info":"PRIME (PRoperty Informed Model of Evolution). Given a set of N amino-acid properties,\n fit a site-level model where non-synonymous rates depend on how much a non-synonymous substitution changes the \n properties of the residue, beta (X,Y) = Exp (log_omega - lambda_1 * diff_1 (X,Y )- lambda_2 * diff_2 (X,Y) -...).\n When lambda_k > 0, changes in property k are disfavored and when lambda_k < 0 -- they are promoted.\n At each site, N tests are performed\n 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. 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":"0.0.1" + }, + "branch attributes":{ + "0":{ + "Node20":{ + "Global MG94xREV":0.001634412628363601, + "Nucleotide GTR":0.001684521619549293 + }, + "Node38":{ + "Global MG94xREV":0.001735516181127408, + "Nucleotide GTR":0.00168484920326581 + }, + "Node4":{ + "Global MG94xREV":0.001634082125054255, + "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":0.001732287226413535, + "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":0.001731614558297581, + "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":0.001735723689760284, + "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":0.001732400224923104, + "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":0.001734572372218793, + "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":0.001735567212797747, + "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":0.001732287290600434, + "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":0.001733756929863212, + "Nucleotide GTR":0.001684431017860219, + "original name":"epi_isl_1589885/hCoV-19/India/WB-1931300250528/2021" + }, + "epi_isl_1592421_hCoV_19_USA_MA_CDC_STM_000044850_2021":{ + "Global 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