Mercurial > repos > iuc > hyphy_bgm
view test-data/busted-out1.json @ 23:ede53272264e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
author | iuc |
---|---|
date | Tue, 20 Apr 2021 10:33:00 +0000 |
parents | cdfa1afd7cb0 |
children | d88bbb287923 |
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which individual sites may have been subject to selection. v2.0 adds support for synonymous rate variation, \nand relaxes the test statistic to 0.5 (chi^2_0 + chi^2_2). Version 2.1 adds a grid search for the initial starting point.\nVersion 2.2 changes the grid search to LHC, and adds an initial search phase to use adaptive Nedler-Mead. Version 3.0 implements the option\nfor branch-site variation in synonymous substitution rates\n", "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})", "version":"3.0" }, "background":0, "branch attributes":{ "0":{ "Baboon":{ "MG94xREV with separate rates for branch sets":0.001771850913718116, "Nucleotide GTR":0.00167976779100812, "constrained":0.0005055252388761481, "original name":"Baboon", "unconstrained":0.0005398732671668005 }, "Cat":{ "MG94xREV with separate rates for branch sets":0.2738959056554072, "Nucleotide GTR":0.266075486389923, "constrained":0.1152712488116292, "original name":"Cat", "unconstrained":0.120218071527276 }, "Chimp":{ "MG94xREV with separate rates for branch sets":0.001827968855137289, "Nucleotide GTR":0.001817801565830578, "constrained":0.0006181497274348637, "original name":"Chimp", "unconstrained":0.0006183542388399873 }, "Cow":{ "MG94xREV with separate rates for branch sets":0.2477119781238836, "Nucleotide GTR":0.2480176045457076, "constrained":0.1036665344622347, "original name":"Cow", "unconstrained":0.1088268022245659 }, "Horse":{ "MG94xREV with separate rates for branch sets":0.211203801568566, "Nucleotide GTR":0.2090856782081004, "constrained":0.08236651201101133, "original name":"Horse", "unconstrained":0.08564084427400141 }, "Human":{ "MG94xREV with separate rates for branch sets":0, "Nucleotide GTR":0, "constrained":0, "original name":"Human", "unconstrained":0 }, "Mouse":{ "MG94xREV with separate rates for branch sets":0.1200702443392807, "Nucleotide GTR":0.1181301915748399, "constrained":0.04601717170435755, "original name":"Mouse", "unconstrained":0.04942545223877414 }, "Node1":{ "MG94xREV with separate rates for branch sets":0.2837967450491412, "Nucleotide GTR":0.2767871391397028, "constrained":0.1295742765519239, "unconstrained":0.1515367890887531 }, "Node12":{ "MG94xREV with separate rates for branch sets":0.01788296579298991, "Nucleotide GTR":0.01784443144961206, "constrained":0.005338125135456628, "unconstrained":0.00572208893382143 }, "Node2":{ "MG94xREV with separate rates for branch sets":0.06423714540466627, "Nucleotide GTR":0.06616183769400197, "constrained":0.02253286838656328, "unconstrained":0.02248978054488407 }, "Node3":{ "MG94xREV with separate rates for branch sets":0.1017201477652066, "Nucleotide GTR":0.09890202668045614, "constrained":0.04280347934583096, "unconstrained":0.04618990784049085 }, "Node8":{ "MG94xREV with separate rates for branch sets":0.1096720572321177, "Nucleotide GTR":0.10624077635158, "constrained":0.04415239867414091, "unconstrained":0.04768889036449767 }, "Node9":{ "MG94xREV with separate rates for branch sets":0.02591275475412757, "Nucleotide GTR":0.02566524291670843, "constrained":0.00997308939110993, "unconstrained":0.009841415288506062 }, "Pig":{ "MG94xREV with separate rates for branch sets":0.1928073761020463, "Nucleotide GTR":0.1871746592118726, "constrained":0.07816490289585476, "original name":"Pig", 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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":"busted.filter.default" } }, "fits":{ "Constrained model":{ "AIC-c":6918.851822592964, "Log Likelihood":-3419.573452280089, "Rate Distributions":{ "Synonymous site-to-site rates":{ "0":{ "proportion":0.3289898788632067, "rate":0.3124849036133048 }, "1":{ "proportion":0.5748197734913485, "rate":1.039520868895482 }, "2":{ "proportion":0.09619034764544485, "rate":3.115265578623139 } }, "Test":{ "0":{ "omega":0, "proportion":0.02093092071081848 }, "1":{ "omega":0, "proportion":0.1387433808480476 }, "2":{ "omega":1, "proportion":0.8403256984411339 } } }, "display order":3, "estimated parameters":39 }, "MG94xREV with separate rates for branch sets":{ "AIC-c":6997.089050462658, "Equilibrium frequencies": [ [0.04875339327772683], [0.03982858547830345], [0.04946803524790992], [0.04152216138298744], [0.01811683453600613], [0.01480036248560469], [0.0183823965708893], [0.01542969784826435], [0.01894694796506697], [0.01547851515238824], [0.01922467805342367], [0.01613668666381816], [0.02832099415740372], [0.02313654621336914], [0.02873613184734657], [0.02412034959764736], [0.01662182431200483], [0.01357902918971745], [0.01686547203528639], [0.01415643148428886], [0.006176695005242439], [0.005045987744654046], 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rate ratio for *test*": [ [0.9950576192409499, 1] ] }, "display order":1, "estimated parameters":31 }, "Nucleotide GTR":{ "AIC-c":7112.85745601076, "Equilibrium frequencies": [ [0.3592490842490842], [0.181959706959707], [0.240018315018315], [0.2187728937728937] ], "Log Likelihood":-3532.321297387654, "Rate Distributions":{ "Substitution rate from nucleotide A to nucleotide C":0.5497129763145497, "Substitution rate from nucleotide A to nucleotide G":1, "Substitution rate from nucleotide A to nucleotide T":0.264666902964203, "Substitution rate from nucleotide C to nucleotide G":0.4916303643305098, "Substitution rate from nucleotide C to nucleotide T":1.027924764411573, "Substitution rate from nucleotide G to nucleotide T":0.304615404570875 }, "display order":0, "estimated parameters":24 }, "Unconstrained model":{ "AIC-c":6910.766610587704, "Log Likelihood":-3414.486640449675, "Rate Distributions":{ "Synonymous site-to-site rates":{ "0":{ "proportion":0.2645541257391169, "rate":0.2747941124675511 }, "1":{ "proportion":0.6325830460054784, "rate":0.9734675888351726 }, "2":{ "proportion":0.1028628282554047, "rate":3.028333913894314 } }, "Test":{ "0":{ "omega":0, "proportion":0.04809457608200497 }, "1":{ "omega":0, "proportion":0.3410012743721951 }, "2":{ "omega":1.89363684081788, "proportion":0.6109041495458 } } }, "display order":2, "estimated parameters":40 } }, "input":{ "file name":"/tmp/tmp7qHfo2/job_working_directory/000/3/working/./busted_input.fa", "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)" } }, "test results":{ "LRT":10.17362366082671, "p-value":0.003088842014430382 }, "tested":{ "0":{ "Baboon":"test", "Cat":"test", "Chimp":"test", "Cow":"test", "Horse":"test", "Human":"test", "Mouse":"test", "Node1":"test", "Node12":"test", "Node2":"test", "Node3":"test", "Node8":"test", "Node9":"test", "Pig":"test", "Rat":"test", "RhMonkey":"test" } }, "timers":{ "Constrained BUSTED model fitting":{ "order":3, "timer":62 }, "Overall":{ "order":0, "timer":228 }, "Preliminary model fitting":{ "order":1, "timer":3 }, "Unconstrained BUSTED model fitting":{ "order":2, "timer":161 } } }