Mercurial > repos > iuc > hyphy_sm19
view test-data/relax-out1.json @ 21:4636d51b049c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d44a94772c58903157edfc12c2a67819cfe252a9"
author | iuc |
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date | Wed, 24 Feb 2021 19:01:45 +0000 |
parents | ae7c42d49717 |
children | 36e40d93e8a3 |
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{ "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 }, "Chimp":{ "original name":"Chimp", "Nucleotide GTR":0.001818722292071369, "MG94xREV with separate rates for branch sets":0.001828056639868651, "General descriptive":0.001850581335499795, "k (general descriptive)":2.329184252362038, "RELAX alternative":0.001831548027528597, "RELAX null":0.001835680183060623, "RELAX partitioned descriptive":0.00183255534978807 }, "Baboon":{ "original name":"Baboon", "Nucleotide GTR":0.001682319705247233, "MG94xREV with separate rates for branch sets":0.001770013551346919, "General descriptive":0.001869883333754939, "k (general descriptive)":0.1228116964827354, "RELAX alternative":0.001867314836287998, "RELAX null":0.001853697678697539, "RELAX partitioned descriptive":0.00189422569191071 }, "RhMonkey":{ "original name":"RhMonkey", "Nucleotide GTR":0.003776495523121213, "MG94xREV with separate rates for branch sets":0.003720554271464007, "General descriptive":0.003663070393385353, "k (general descriptive)":2.272939790126477, "RELAX alternative":0.003641537789305734, "RELAX null":0.003670955010908306, "RELAX partitioned descriptive":0.003632158699516803 }, "Cow":{ "original name":"Cow", "Nucleotide GTR":0.2483201583381086, "MG94xREV with separate rates for branch sets":0.2522875145085426, "General descriptive":0.3735091756053704, "k (general descriptive)":1.19957642031092, "RELAX alternative":0.3407703477665083, "RELAX null":0.2958310860090909, "RELAX partitioned descriptive":0.3460604457589064 }, "Pig":{ "original name":"Pig", "Nucleotide GTR":0.1871417867164377, "MG94xREV with separate rates for branch sets":0.1903173961963296, "General descriptive":0.2109384940367451, "k (general descriptive)":0.6656155688777629, "RELAX alternative":0.197167672065417, "RELAX null":0.2182629931612711, "RELAX partitioned descriptive":0.2076369268997903 }, "Horse":{ "original name":"Horse", "Nucleotide GTR":0.2091567334932583, "MG94xREV with separate rates for branch sets":0.2159358728261337, "General descriptive":0.2810540078141565, "k (general descriptive)":0.8115699858212525, "RELAX alternative":0.3032889682089364, "RELAX null":0.2571098559672552, "RELAX partitioned descriptive":0.3026705354406338 }, "Cat":{ "original name":"Cat", "Nucleotide GTR":0.2660040109418023, "MG94xREV with separate rates for branch sets":0.2795692100037539, "General descriptive":0.3635335087937213, "k (general descriptive)":0.9728289997736356, "RELAX alternative":0.3660889485578829, "RELAX null":0.3281803512051322, "RELAX partitioned descriptive":0.370631318143086 }, "Mouse":{ "original name":"Mouse", "Nucleotide GTR":0.1182531454610134, "MG94xREV with separate rates for branch sets":0.1199409901922202, "General descriptive":0.1313354563273305, "k (general descriptive)":0.2294495132372282, "RELAX alternative":0.1341640738853253, "RELAX null":0.1483938193994467, "RELAX partitioned descriptive":0.1476318125310598 }, "Rat":{ "original name":"Rat", "Nucleotide GTR":0.06669544716210057, "MG94xREV with separate rates for branch sets":0.06725647453745125, "General descriptive":0.07175915155128718, "k (general descriptive)":0.5208088414555363, "RELAX alternative":0.0724007498013708, "RELAX null":0.07365614414375878, "RELAX partitioned descriptive":0.07568744563050285 }, "Node1":{ "Nucleotide GTR":0.2771601504028877, "MG94xREV with separate rates for branch sets":0.286127507474972, "General descriptive":0.3532216661512288, "k (general descriptive)":0.2199586786715634, "RELAX alternative":0.3833004811985787, "RELAX null":0.4576044234710181, "RELAX partitioned descriptive":0.4360897576025625 }, "Node12":{ "Nucleotide GTR":0.01783222754921504, "MG94xREV with separate rates for branch sets":0.01799298835381691, "General descriptive":0.01771170858901891, "k (general descriptive)":0.1560499010177516, "RELAX alternative":0.01833338832069913, "RELAX null":0.01828012634520382, "RELAX partitioned descriptive":0.01877701767421286 }, "Node2":{ "Nucleotide GTR":0.06619118337434968, "MG94xREV with separate rates for branch sets":0.06192085035608558, "General descriptive":0.05843310574046084, "k (general descriptive)":0.2816499194095207, "RELAX alternative":0.05469841675490748, "RELAX null":0.06219694236954142, "RELAX partitioned descriptive":0.06011281230238084 }, "Node3":{ "Nucleotide GTR":0.09883746945145887, "MG94xREV with separate rates for branch sets":0.09744342239018626, "General descriptive":0.1340338084149808, "k (general descriptive)":0.8358980179450297, "RELAX alternative":0.1164056814082033, "RELAX null":0.1282588343299434, "RELAX partitioned descriptive":0.1194563668460339 }, "Node8":{ "Nucleotide GTR":0.106110061225871, "MG94xREV with separate rates for branch sets":0.1090208137603471, "General descriptive":0.1401594332730181, "k (general descriptive)":0.9135621448569878, "RELAX alternative":0.1275155316795084, "RELAX null":0.1346842719904758, "RELAX partitioned descriptive":0.1358683972849559 }, "Node9":{ "Nucleotide GTR":0.02567391471029082, "MG94xREV with separate rates for branch sets":0.02582385148170195, "General descriptive":0.02665352479510937, "k (general descriptive)":0.1089752436854629, "RELAX alternative":0.02681134359856903, "RELAX null":0.02759760291393045, "RELAX partitioned descriptive":0.02746061131173372 } }, "attributes":{ "original name":{ "attribute type":"node label", "display order":-1 }, "Nucleotide GTR":{ "attribute type":"branch length", "display order":0 }, "MG94xREV with separate rates for branch sets":{ "attribute type":"branch length", "display order":1 }, "General descriptive":{ "attribute type":"branch length", "display order":4 }, "k (general descriptive)":{ "attribute type":"branch label", "display order":4 }, "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 } } } }