Mercurial > repos > iuc > hyphy_fubar
view test-data/relax-out1.json @ 34:6e72195b364a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 821e0f3e4546bc55e093ab63bd9f9b57f2bf772d
author | iuc |
---|---|
date | Thu, 18 Aug 2022 14:00:13 +0000 |
parents | 55a45d4c31dc |
children |
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{ "analysis":0, "branch attributes":{ "0":{ "Baboon":{ "General descriptive":0.001859058366368826, "MG94xREV with separate rates for branch sets":0.001769294089885709, "Nucleotide GTR":0.001685167654714891, "RELAX alternative":0.001873708670384941, "RELAX null":0.001859167714920677, "RELAX partitioned descriptive":0.001898817195216417, "k (general descriptive)":0.09969742933359635, "original name":"Baboon" }, "Cat":{ "General descriptive":0.3650161006190072, "MG94xREV with separate rates for branch sets":0.2796018473093496, "Nucleotide GTR":0.2660536011315811, "RELAX alternative":0.3685874431614762, "RELAX null":0.3167334440346762, "RELAX partitioned descriptive":0.3719472357609613, "k (general descriptive)":2.319877215422834, "original name":"Cat" }, "Chimp":{ "General descriptive":0.001895983937468787, "MG94xREV with separate rates for branch sets":0.001826027667597702, "Nucleotide GTR":0.001820258053351119, "RELAX alternative":0.001831530791728368, "RELAX null":0.001834052740714585, "RELAX partitioned descriptive":0.001832682515795942, "k (general descriptive)":5.158328270628251, "original name":"Chimp" }, "Cow":{ "General descriptive":0.3737128696500712, "MG94xREV with separate rates for branch sets":0.2521304147607955, "Nucleotide GTR":0.2480198736772598, "RELAX alternative":0.3426997068768813, "RELAX null":0.2931467439343907, "RELAX partitioned descriptive":0.3469082289876269, "k (general descriptive)":2.852150041266453, "original name":"Cow" }, "Horse":{ "General descriptive":0.2804279827409984, "MG94xREV with separate rates for branch sets":0.2158535884657318, "Nucleotide GTR":0.2090998951755368, "RELAX alternative":0.3058441352816696, "RELAX null":0.2546949756245578, "RELAX partitioned descriptive":0.3035514182923183, "k (general descriptive)":1.929916608813313, "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)":1.485684693044203, "original name":"Human" }, "Mouse":{ "General descriptive":0.1308809509233143, "MG94xREV with separate rates for branch sets":0.1197584101055861, "Nucleotide GTR":0.1181058300538561, "RELAX alternative":0.1346294129227689, "RELAX null":0.1438267359449897, "RELAX partitioned descriptive":0.148454172127534, "k (general descriptive)":0.4625550584398252, "original name":"Mouse" }, "Node1":{ "General descriptive":0.3500691487967139, "MG94xREV with separate rates for branch sets":0.2856782993656827, "Nucleotide GTR":0.2767105173979571, "RELAX alternative":0.385503346940632, "RELAX null":0.4352096867868785, "RELAX partitioned descriptive":0.4379872513902164, "k (general descriptive)":0.4572754180074107 }, "Node12":{ "General descriptive":0.01767932040676307, "MG94xREV with separate rates for branch sets":0.01800350744117403, "Nucleotide GTR":0.01784222107494562, "RELAX alternative":0.01834159481548459, "RELAX 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null":0.1334227466998376, "RELAX partitioned descriptive":0.1367904558404228, "k (general descriptive)":2.206967022203622 }, "Node9":{ "General descriptive":0.02664133794298214, "MG94xREV with separate rates for branch sets":0.02578742148415842, "Nucleotide GTR":0.02567813733543303, "RELAX alternative":0.02680940150436639, "RELAX null":0.0273694783141817, "RELAX partitioned descriptive":0.02747376898615263, "k (general descriptive)":0.07343731037788495 }, "Pig":{ "General descriptive":0.210591346560755, "MG94xREV with separate rates for branch sets":0.1903463787974325, "Nucleotide GTR":0.1871390433004313, "RELAX alternative":0.1974790507889271, "RELAX null":0.2130024973755621, "RELAX partitioned descriptive":0.2084407457285946, "k (general descriptive)":1.581210670484469, "original name":"Pig" }, "Rat":{ "General descriptive":0.07157977734335202, "MG94xREV with separate rates for branch sets":0.06709765698107663, "Nucleotide GTR":0.06661490534189227, "RELAX alternative":0.07252374836036582, "RELAX null":0.0734705682786943, "RELAX partitioned descriptive":0.0757525093290258, "k (general descriptive)":1.316568267879453, "original name":"Rat" }, "RhMonkey":{ "General descriptive":0.003672848089716511, "MG94xREV with separate rates for branch sets":0.003717350789869306, "Nucleotide GTR":0.003778804730491441, "RELAX alternative":0.003633278464154418, "RELAX null":0.003661271320845124, "RELAX partitioned descriptive":0.003625957794514879, "k (general descriptive)":5.196295069596697, "original name":"RhMonkey" } }, "attributes":{ "General descriptive":{ "attribute type":"branch length", "display order":4 }, "MG94xREV with separate rates for branch sets":{ "attribute type":"branch length", "display order":1 }, "Nucleotide GTR":{ "attribute type":"branch length", "display order":0 }, "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 }, "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":{ "AIC-c":6945.892677835464, "Log Likelihood":-3420.487593043145, "Rate Distributions":{ "Shared":{ "0":{ "omega":2.201451464048879e-18, "proportion":0.3073650505039141 }, "1":{ "omega":2.201451464048879e-18, "proportion":0.2383891488636319 }, "2":{ "omega":2.201451281679838, "proportion":0.4542458006324541 } } }, "display order":4, "estimated parameters":51 }, "MG94xREV with separate rates for branch sets":{ "AIC-c":6987.566513560764, "Equilibrium frequencies": [ [0.04876086397632926], [0.03982224127745371], [0.0494959405650269], [0.04152830682371345], [0.01810345074594235], [0.01478480742075003], [0.01837636270304883], [0.01541821854326533], [0.01892910005547028], [0.01545910240515689], [0.01921445878706794], [0.01612140169177368], [0.02829747763884322], [0.02311011106415996], [0.02872406592369408], [0.02410019507229243], [0.01663805943190806], [0.01358804506433061], [0.01688888041768248], [0.01417018446135155], [0.006177213955434187], [0.005044834822351987], [0.006270336287397383], [0.00526096577332031], [0.006458939937330408], [0.005274916061901906], [0.006556309326397028], [0.005500904159606446], [0.009655594186286731], [0.007885574003572761], [0.009801153568494354], [0.008223407979974132], [0.03327785448210915], [0.02717750758119989], [0.03377952261833742], [0.02834184710178207], [0.01235507229404208], [0.01009019590244688], [0.01254132667213156], [0.01052248035033209], [0.01291855364640413], [0.01055038238273567], [0.01311330258173711], [0.01100238215235291], [0.01931219560697892], [0.0157719705998612], [0.01960332955558842], [0.01644767379420349], [0.01965132601881859], [0.02049322866376102], [0.008933621043463411], [0.007295949736387736], [0.009068296583349953], [0.007608523013862737], [0.007628698224327205], [0.009481877006094248], [0.00795552712159237], [0.01396413011303752], [0.01140428846505027], [0.01417464125436193], [0.01189287130232129] ], "Log Likelihood":-3461.208406480981, "Rate Distributions":{ "non-synonymous/synonymous rate ratio for *Reference*": [ [0.7685912547191639, 1] ], "non-synonymous/synonymous rate ratio for *Test*": [ [1.603198088111489, 1] ] }, "display order":1, "estimated parameters":32 }, "Nucleotide GTR":{ "AIC-c":7112.857288723968, "Equilibrium frequencies": [ [0.3592490842490842], [0.181959706959707], [0.240018315018315], [0.2187728937728937] ], "Log Likelihood":-3532.321213744258, "Rate Distributions":{ "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087, "Substitution rate from nucleotide A to nucleotide G":1, "Substitution rate from nucleotide A to nucleotide T":0.2646800222727828, "Substitution rate from nucleotide C to nucleotide G":0.4918071762416347, "Substitution rate from nucleotide C to nucleotide T":1.028675134787727, "Substitution rate from nucleotide G to nucleotide T":0.3045013055839741 }, "display order":0, "estimated parameters":24 }, "RELAX alternative":{ "AIC-c":6931.926773483473, "Log Likelihood":-3429.236709163995, "Rate Distributions":{ "Reference":{ "0":{ "omega":1.761161171239182e-19, "proportion":0.2691773911207853 }, "1":{ "omega":1.762922332410267e-19, "proportion":0.2692122656891806 }, "2":{ "omega":2.208286837998088, "proportion":0.4616103431900341 } }, "Test":{ "0":{ "omega":1.673670300056362e-44, "proportion":0.2691773911207853 }, "1":{ "omega":1.677579612236672e-44, "proportion":0.2692122656891806 }, "2":{ "omega":6.354762788556926, "proportion":0.4616103431900341 } } }, "display order":2, "estimated parameters":36 }, "RELAX null":{ "AIC-c":6946.648596594286, "Log Likelihood":-3437.63727539638, "Rate Distributions":{ "Reference":{ "0":{ "omega":1.408928936991542e-20, "proportion":0.265244047162938 }, "1":{ "omega":1.410337865928411e-20, "proportion":0.28512630848952 }, "2":{ "omega":3.213510017765925, "proportion":0.4496296443475419 } }, "Test":{ "0":{ "omega":1.408928936991542e-20, "proportion":0.265244047162938 }, "1":{ "omega":1.410337865928411e-20, "proportion":0.28512630848952 }, "2":{ "omega":3.213510017765925, "proportion":0.4496296443475419 } } }, "display order":3, "estimated parameters":35 }, "RELAX partitioned descriptive":{ "AIC-c":6937.049237937651, "Log Likelihood":-3427.627954124649, "Rate Distributions":{ "Reference":{ "0":{ "omega":0.1847557016619168, "proportion":0.4766160247339328 }, "1":{ "omega":0.3367540359539261, "proportion":0.3005513276312735 }, "2":{ "omega":4.272816072857538, "proportion":0.2228326476347937 } }, "Test":{ "0":{ "omega":1.127143149593234e-21, "proportion":0.2367540589657237 }, "1":{ "omega":1.128270292740756e-21, "proportion":0.2771164325302933 }, "2":{ "omega":6.023626417874829, "proportion":0.4861295085039831 } } }, "display order":5, "estimated parameters":40 } }, "input":{ "file name":"/tmp/tmpkgsdjj1d/job_working_directory/000/3/working/./input.fasta", "number of sequences":10, "number of sites":187, "partition count":1, "trees":{ "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.08509899999999999,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)" } }, "runtime":"2.5.32", "test results":{ "LRT":16.80113246476958, "p-value":4.150852429507523e-05, "relaxation or intensification parameter":2.334214628944839 }, "tested":{ "0":{ "Baboon":"Reference", "Cat":"Test", "Chimp":"Reference", "Cow":"Test", "Horse":"Test", "Human":"Reference", "Mouse":"Reference", "Node1":"Reference", "Node12":"Reference", "Node2":"Reference", "Node3":"Reference", "Node8":"Reference", "Node9":"Reference", "Pig":"Reference", "Rat":"Reference", "RhMonkey":"Reference" } }, "timers":{ "General descriptive model fitting":{ "order":2, "timer":127 }, "Overall":{ "order":0, "timer":396 }, "Preliminary model fitting":{ "order":1, "timer":8 }, "RELAX alternative model fitting":{ "order":3, "timer":103 }, "RELAX null model fitting":{ "order":4, "timer":41 }, "RELAX partitioned descriptive":{ "order":5, "timer":116 } } }