Mercurial > repos > iuc > hyphy_conv
diff test-data/relax-out1.json @ 0:9ce3d6d4bd0e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
| author | iuc |
|---|---|
| date | Tue, 20 Apr 2021 10:31:50 +0000 |
| parents | |
| children | f6e7b5955712 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/relax-out1.json Tue Apr 20 10:31:50 2021 +0000 @@ -0,0 +1,499 @@ +{ + "analysis":{ + "info":"RELAX (a random effects test of selection relaxation) uses a random effects branch-site model framework to test whether a set of 'Test' branches evolves under relaxed selection relative to a set of 'Reference' branches (R), as measured by the relaxation parameter (K).\n Version 2.1 adds a check for stability in K estimates to try to mitigate convergence problems", + "version":"2.1", + "citation":"RELAX: Detecting Relaxed Selection in a Phylogenetic Framework (2015). Mol Biol Evol 32 (3): 820-832", + "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group", + "contact":"spond@temple.edu", + "requirements":"in-frame codon alignment and a phylogenetic tree, with at least two groups of branches defined using the {} notation (one group can be defined as all unlabeled branches)" + }, + "input":{ + "file name":"/home/galaxystaging/galaxy/database/jobs_directory/000/79/working/relax_input.fa", + "number of sequences":10, + "number of sites":187, + "partition count":1, + "trees":{ + "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.085099,Horse:0.165787,Cat:0.264806)Node2:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node9:0.022733,(Human:0.004349,Chimp:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,Rat:0.050958,Mouse:0.09795)" + } + }, + "fits":{ + "Nucleotide GTR":{ + "Log Likelihood":-3531.964032193222, + "estimated parameters":24, + "AIC-c":7112.142925621896, + "Equilibrium frequencies":[ + [0.3563279857397504], + [0.1837789661319073], + [0.2402852049910873], + [0.2196078431372549] + ], + "Rate Distributions":{ + "Substitution rate from nucleotide A to nucleotide C":0.5465757107930838, + "Substitution rate from nucleotide A to nucleotide G":1, + "Substitution rate from nucleotide A to nucleotide T":0.264131123736109, + "Substitution rate from nucleotide C to nucleotide G":0.4861812992450388, + "Substitution rate from nucleotide C to nucleotide T":1.017887589835735, + "Substitution rate from nucleotide G to nucleotide T":0.3021773696987065 + }, + "display order":0 + }, + "MG94xREV with separate rates for branch sets":{ + "Log Likelihood":-3460.931903299487, + "estimated parameters":32, + "AIC-c":6987.013507197776, + "Equilibrium frequencies":[ + [0.04785168648208005], + [0.03911346079312019], + [0.04842054060317301], + [0.04069665666515385], + [0.01817010744778396], + [0.01485205303123071], + [0.01838611113045968], + [0.01545321970309948], + [0.0190138898893362], + [0.01554175184587827], + [0.01923992433904378], + [0.01617083546230154], + [0.02796925133965702], + [0.02286176927319543], + [0.02830174586718859], + [0.02378714529482007], + [0.01687870337957799], + [0.01379647304851128], + [0.01707935503225849], + [0.01435491300079667], + [0.006409133648843443], + [0.005238757839512795], + [0.006485324528555602], + [0.005450807083377185], + [0.006706760641638982], + [0.005482034985409045], + [0.006786489669196017], + [0.005703931360295163], + [0.009865581170012171], + [0.008064021368173151], + [0.009982861811889655], + [0.008390428826966174], + [0.03287895020631181], + [0.02687490503171972], + [0.033269810543681], + [0.0279627207822247], + [0.01248470225271473], + [0.01020486315060615], + [0.01263311863778268], + [0.01061792547971484], + [0.01306446616325414], + [0.01067875601941112], + [0.01321977470017749], + [0.01111100011404158], + [0.01921770557551369], + [0.01570834862514353], + [0.01944616295744266], + [0.01634417558076203], + [0.01975257768318274], + [0.02055210293142003], + [0.009176034326710849], + [0.007500393094996483], + [0.00928511773266342], + [0.007803986567571961], + [0.00784869593340758], + [0.009716299514778986], + [0.008166387662818644], + [0.01412467213650941], + [0.01154535713247913], + [0.01429258425298098], + [0.01201267864744234] + ], + "Rate Distributions":{ + "non-synonymous/synonymous rate ratio for *Reference*":[ + [1.617765969026557, 1] + ], + "non-synonymous/synonymous rate ratio for *Test*":[ + [0.7687683974183303, 1] + ] + }, + "display order":1 + }, + "General descriptive":{ + "Log Likelihood":-3420.975369746331, + "estimated parameters":51, + "AIC-c":6946.868231241836, + "Rate Distributions":{ + "Shared":{ + "0":{ + "omega":1e-08, + "proportion":0.2345034364701236 + }, + "1":{ + "omega":1e-08, + "proportion":0.3180344596999608 + }, + "2":{ + "omega":6.64943557055033, + "proportion":0.4474621038299156 + } + } + }, + "display order":4 + }, + "RELAX alternative":{ + "Log Likelihood":-3429.125323833579, + "estimated parameters":36, + "AIC-c":6931.704002822642, + "Rate Distributions":{ + "Test":{ + "0":{ + "omega":0, + "proportion":0.1993913071931658 + }, + "1":{ + "omega":0, + "proportion":0.3360341729181165 + }, + "2":{ + "omega":2.153056268947235, + "proportion":0.4645745198887177 + } + }, + "Reference":{ + "0":{ + "omega":0, + "proportion":0.1993913071931658 + }, + "1":{ + "omega":0, + "proportion":0.3360341729181165 + }, + "2":{ + "omega":6.166712663934246, + "proportion":0.4645745198887177 + } + } + }, + "display order":2 + }, + "RELAX null":{ + "Log Likelihood":-3437.187429488768, + "estimated parameters":35, + "AIC-c":6945.748904779063, + "Rate Distributions":{ + "Test":{ + "0":{ + "omega":0.1177689533662908, + "proportion":0.4926494715348529 + }, + "1":{ + "omega":0.3195682613972807, + "proportion":0.1517366025099117 + }, + "2":{ + "omega":3.893733071412322, + "proportion":0.3556139259552353 + } + }, + "Reference":{ + "0":{ + "omega":0.1177689533662908, + "proportion":0.4926494715348529 + }, + "1":{ + "omega":0.3195682613972807, + "proportion":0.1517366025099117 + }, + "2":{ + "omega":3.893733071412322, + "proportion":0.3556139259552353 + } + } + }, + "display order":3 + }, + "RELAX partitioned descriptive":{ + "Log Likelihood":-3427.515821600644, + "estimated parameters":40, + "AIC-c":6936.824972889643, + "Rate Distributions":{ + "Test":{ + "0":{ + "omega":0.2264899618249929, + "proportion":0.1370778077745601 + }, + "1":{ + "omega":0.2328054750512875, + "proportion":0.6322930022247097 + }, + "2":{ + "omega":4.13407071706127, + "proportion":0.2306291900007301 + } + }, + "Reference":{ + "0":{ + "omega":0, + "proportion":0.09054841512283768 + }, + "1":{ + "omega":0, + "proportion":0.4231976237742962 + }, + "2":{ + "omega":5.975493863572218, + "proportion":0.4862539611028661 + } + } + }, + "display order":5 + } + }, + "timers":{ + "Overall":{ + "timer":562, + "order":0 + }, + "Preliminary model fitting":{ + "timer":33, + "order":1 + }, + "General descriptive model fitting":{ + "timer":256, + "order":2 + }, + "RELAX alternative model fitting":{ + "timer":78, + "order":3 + }, + "RELAX null model fitting":{ + "timer":98, + "order":4 + }, + "RELAX partitioned descriptive":{ + "timer":95, + "order":5 + } + }, + "test results":{ + "LRT":16.12421131037809, + "p-value":5.932080525117289e-05, + "relaxation or intensification parameter":0.4215604262166031 + }, + "tested":{ + "0":{ + "Pig":"Test", + "Cow":"Reference", + "Node3":"Test", + "Horse":"Reference", + "Cat":"Reference", + "Node2":"Test", + "RhMonkey":"Test", + "Baboon":"Test", + "Node9":"Test", + "Human":"Test", + "Chimp":"Test", + "Node12":"Test", + "Node8":"Test", + "Node1":"Test", + "Rat":"Test", + "Mouse":"Test" + } + }, + "data partitions":{ + "0":{ + "name":"relax.filter.default", + "coverage":[ + [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 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] + ] + } + }, + "branch attributes":{ + "0":{ + "Human":{ + "original name":"Human", + "Nucleotide GTR":0, + "MG94xREV with separate rates for branch sets":0, + "General descriptive":0, + "k (general descriptive)":0.7168352052656061, + "RELAX alternative":0, + "RELAX null":0, + "RELAX partitioned descriptive":0 + 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}, + "RELAX alternative":{ + "attribute type":"branch length", + "display order":2 + }, + "RELAX null":{ + "attribute type":"branch length", + "display order":3 + }, + "RELAX partitioned descriptive":{ + "attribute type":"branch length", + "display order":5 + } + } + } +} \ No newline at end of file