Mercurial > repos > iuc > hyphy_annotate
diff test-data/relax-out1.json @ 2:a88848771d2d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
| author | iuc |
|---|---|
| date | Tue, 27 Apr 2021 18:01:42 +0000 |
| parents | df56795c3d89 |
| children | e6009f23582c |
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--- a/test-data/relax-out1.json Tue Apr 20 19:53:07 2021 +0000 +++ b/test-data/relax-out1.json Tue Apr 27 18:01:42 2021 +0000 @@ -1,486 +1,174 @@ { - "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] - ] - } - }, + "analysis":0, "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 + "General descriptive":0.001858767762813579, + "MG94xREV with separate rates for branch sets":0.001769472024099301, + "Nucleotide GTR":0.001680040630127455, + "RELAX alternative":0.001872256662230973, + "RELAX null":0.001855569334462731, + "RELAX partitioned descriptive":0.001898170574782418, + "k (general descriptive)":0.09971581394819819, + "original name":"Baboon" }, "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 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null":0.2948256709356563, + "RELAX partitioned descriptive":0.3466331923230422, + "k (general descriptive)":2.846155982935764, + "original name":"Cow" + }, + "Horse":{ + "General descriptive":0.2802176313870697, + "MG94xREV with separate rates for branch sets":0.2158304510870495, + "Nucleotide GTR":0.2090310577070883, + "RELAX alternative":0.3058487498567987, + "RELAX null":0.2559911331878715, + "RELAX partitioned descriptive":0.3034694616209482, + "k (general descriptive)":1.926646959057857, + "original name":"Horse" + }, + "Human":{ + "General descriptive":0, + "MG94xREV with separate rates for branch sets":0, + "Nucleotide GTR":0, + "RELAX alternative":0, + "RELAX null":0, + "RELAX partitioned descriptive":0, + "k (general descriptive)":1.462532487172471, + "original name":"Human" }, "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 + "General descriptive":0.1307950021191255, + "MG94xREV with separate rates for branch sets":0.1197727080219867, + "Nucleotide GTR":0.1180171198334285, + "RELAX alternative":0.1346501492117481, + "RELAX null":0.1468861666244963, + "RELAX partitioned descriptive":0.1475623398849678, + "k (general descriptive)":0.4639609139295889, + "original name":"Mouse" }, "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 + "General descriptive":0.350050900813081, + "MG94xREV with separate rates for branch sets":0.2857356440257563, + "Nucleotide GTR":0.2767237570684924, + "RELAX alternative":0.3856490868629754, + "RELAX null":0.4521046025119397, + "RELAX partitioned descriptive":0.4358952685746469, + "k (general descriptive)":0.458870761901378 }, "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 + "General descriptive":0.01766384491594095, + "MG94xREV with separate rates for branch sets":0.01800001211221997, + "Nucleotide GTR":0.01784803874223016, + "RELAX alternative":0.01835132674304535, + "RELAX null":0.0182458522959868, + "RELAX partitioned descriptive":0.01878351896299688, + "k (general descriptive)":0.1241597340554799 }, "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 + "General descriptive":0.05771641706257456, + "MG94xREV with separate rates for branch sets":0.06169547093990335, + "Nucleotide GTR":0.06613162123865737, + "RELAX alternative":0.05450381496370671, + "RELAX null":0.06144358908741494, + "RELAX partitioned descriptive":0.05974179966710006, + "k (general descriptive)":0.5400661932123572 }, "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 + "General descriptive":0.133048972566238, + "MG94xREV with separate rates for branch sets":0.09736816312927643, + "Nucleotide GTR":0.09886326330774685, + "RELAX alternative":0.1168284793254293, + "RELAX null":0.1276889506286756, + "RELAX partitioned descriptive":0.1195376339442456, + "k (general descriptive)":1.980345386854111 }, "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 + "General descriptive":0.1404364853762839, + "MG94xREV with separate rates for branch sets":0.1092041281639667, + "Nucleotide GTR":0.106239268140425, + "RELAX alternative":0.1283918913740865, + "RELAX null":0.1343238120118072, + "RELAX partitioned descriptive":0.1363833239244288, + "k (general descriptive)":2.210166852936262 }, "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 + "General descriptive":0.02665050120918479, + "MG94xREV with separate rates for branch sets":0.02578196090462333, + "Nucleotide GTR":0.02566573875750134, + "RELAX alternative":0.02679622227446188, + "RELAX null":0.02754241929890747, + "RELAX partitioned descriptive":0.0274479920792393, + "k (general descriptive)":0.0733131770696667 + }, + "Pig":{ + "General descriptive":0.2104601216238473, + "MG94xREV with separate rates for branch sets":0.1902977811335351, + "Nucleotide GTR":0.1871893456388788, + "RELAX alternative":0.19752905148822, + "RELAX null":0.2165309177979844, + "RELAX partitioned descriptive":0.2074828949843082, + "k (general descriptive)":1.577441472516679, + "original name":"Pig" + }, + "Rat":{ + "General descriptive":0.07164210204456434, + "MG94xREV with separate rates for branch sets":0.06709541225974219, + "Nucleotide GTR":0.06661283005976348, + "RELAX alternative":0.07247047023746757, + "RELAX null":0.07343093575256582, + "RELAX partitioned descriptive":0.07560655472076994, + "k (general descriptive)":1.318174884032695, + "original name":"Rat" + }, + "RhMonkey":{ + "General descriptive":0.003674505194636419, + "MG94xREV with separate rates for branch sets":0.003716165486244973, + "Nucleotide GTR":0.003775170135617877, + "RELAX alternative":0.003636176595806718, + "RELAX null":0.003665938723426083, + "RELAX partitioned descriptive":0.003624376345656283, + "k (general descriptive)":5.171610533872274, + "original name":"RhMonkey" } }, "attributes":{ - "original name":{ - "attribute type":"node label", - "display order":-1 - }, - "Nucleotide GTR":{ + "General descriptive":{ "attribute type":"branch length", - "display order":0 + "display order":4 }, "MG94xREV with separate rates for branch sets":{ "attribute type":"branch length", "display order":1 }, - "General descriptive":{ + "Nucleotide GTR":{ "attribute type":"branch length", - "display order":4 - }, - "k (general descriptive)":{ - "attribute type":"branch label", - "display order":4 + "display order":0 }, "RELAX alternative":{ "attribute type":"branch length", @@ -493,7 +181,312 @@ "RELAX partitioned descriptive":{ "attribute type":"branch length", "display order":5 + }, + "k (general descriptive)":{ + "attribute type":"branch label", + "display order":4 + }, + "original name":{ + "attribute type":"node label", + "display order":-1 } } + }, + "data partitions":{ + "0":{ + "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] + ], + "name":"relax.filter.default" + } + }, + "fits":{ + "General descriptive":{ + 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