Mercurial > repos > iuc > hyphy_bgm
view test-data/busted-out1.json @ 33:5b6b8b08f1a9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
author | iuc |
---|---|
date | Wed, 30 Mar 2022 00:17:25 +0000 |
parents | d88bbb287923 |
children |
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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. Version 3.1 adds HMM auto-correlation option for SRV, and binds SRV distributions for multiple branch sets\n", "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})", "version":"3.1" }, "background":0, "branch attributes":{ "0":{ "Baboon":{ "MG94xREV with separate rates for branch sets":0.001772434847524003, "Nucleotide GTR":0.001680040630127455, "constrained":0.001513413708231178, "original name":"Baboon", "unconstrained":0.00161713005248515 }, "Cat":{ "MG94xREV with separate rates for branch sets":0.2735065373507703, "Nucleotide GTR":0.2660909938917123, "constrained":0.3466844629529476, "original name":"Cat", "unconstrained":0.3607268493024173 }, "Chimp":{ "MG94xREV with separate rates for branch sets":0.001828401123834132, "Nucleotide GTR":0.001818373670119325, "constrained":0.001854421055569225, "original name":"Chimp", "unconstrained":0.001853794709397617 }, "Cow":{ "MG94xREV with separate rates for branch sets":0.2477981038577003, "Nucleotide GTR":0.2481025999892287, "constrained":0.3115800338446564, "original name":"Cow", "unconstrained":0.3266266518611717 }, "Horse":{ "MG94xREV with separate rates for branch sets":0.21116782461044, "Nucleotide GTR":0.2090310577070883, "constrained":0.2473423214593362, "original name":"Horse", "unconstrained":0.2568895651944081 }, "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":0.1200804161847832, "Nucleotide GTR":0.1180171198334285, "constrained":0.1381882260320684, "original name":"Mouse", "unconstrained":0.1482500840848965 }, "Node1":{ "MG94xREV with separate rates for branch sets":0.2841417945012228, "Nucleotide GTR":0.2767237570684924, "constrained":0.3893703941610758, "unconstrained":0.4535373691584812 }, "Node12":{ "MG94xREV with separate rates for branch sets":0.01789005959388253, "Nucleotide GTR":0.01784803874223016, "constrained":0.01603697675468384, "unconstrained":0.01716581823757766 }, "Node2":{ "MG94xREV with separate rates for branch sets":0.06425321743363792, "Nucleotide GTR":0.06613162123865737, "constrained":0.06766882319669908, "unconstrained":0.06748821329187271 }, "Node3":{ "MG94xREV with separate rates for branch sets":0.1017634409613201, "Nucleotide GTR":0.09886326330774685, "constrained":0.128627313187861, "unconstrained":0.1385358286963005 }, "Node8":{ "MG94xREV with separate rates for branch sets":0.1095532710088725, "Nucleotide GTR":0.106239268140425, "constrained":0.1326559254556453, "unconstrained":0.1430782720540034 }, "Node9":{ "MG94xREV with separate rates for branch sets":0.02590764371262369, "Nucleotide GTR":0.02566573875750134, "constrained":0.02991066003065707, "unconstrained":0.02952913741456189 }, "Pig":{ "MG94xREV with separate rates for branch sets":0.1925158663261413, "Nucleotide GTR":0.1871893456388788, "constrained":0.2351007649069627, "original name":"Pig", "unconstrained":0.248176820169511 }, "Rat":{ "MG94xREV with separate rates for branch sets":0.06699144002108472, "Nucleotide GTR":0.06661283005976348, "constrained":0.06832918896283274, "original name":"Rat", "unconstrained":0.07114161288708017 }, "RhMonkey":{ "MG94xREV with separate rates for branch sets":0.003716234330029482, "Nucleotide GTR":0.003775170135617877, "constrained":0.004078975866589158, "original name":"RhMonkey", "unconstrained":0.003977618821878279 } }, "attributes":{ "MG94xREV with separate rates for branch sets":{ "attribute type":"branch length", "display order":1 }, "Nucleotide GTR":{ "attribute type":"branch length", "display order":0 }, "constrained":{ "attribute type":"branch length", "display order":1 }, "original name":{ "attribute type":"node label", "display order":0 }, "unconstrained":{ "attribute type":"branch length", "display order":0 } } }, "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":"busted.filter.default" } }, "fits":{ "Constrained model":{ "AIC-c":6918.865252134614, "Log Likelihood":-3419.580167050914, "Rate Distributions":{ "Synonymous site-to-site rates":{ "0":{ "proportion":0.3286044813984554, "rate":0.3114745230555425 }, "1":{ "proportion":0.5759073485616787, "rate":1.038727366194607 }, "2":{ "proportion":0.09548817003986594, "rate":3.135858111155513 } }, "Test":{ "0":{ "omega":0, "proportion":0.1610337459523823 }, "1":{ "omega":0.9239856235614761, "proportion":0 }, "2":{ "omega":1, "proportion":0.8389662540476177 } } }, "display order":3, "estimated parameters":39 }, "MG94xREV with separate rates for branch sets":{ "AIC-c":6997.104847699299, "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], 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rate ratio for *test*": [ [0.9959842858928788, 1] ] }, "display order":1, "estimated parameters":31 }, "Nucleotide GTR":{ "AIC-c":7112.857310169033, "Equilibrium frequencies": [ [0.3592490842490842], [0.181959706959707], [0.240018315018315], [0.2187728937728937] ], "Log Likelihood":-3532.32122446679, "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":0.2647746107611847, "Substitution rate from nucleotide C to nucleotide G":0.4917423221832032, "Substitution rate from nucleotide C to nucleotide T":1.02837595903795, "Substitution rate from nucleotide G to nucleotide T":0.304509117524575 }, "display order":0, "estimated parameters":24 }, "Unconstrained model":{ "AIC-c":6910.776988890891, "Log Likelihood":-3414.491829601268, "Rate Distributions":{ "Synonymous site-to-site rates":{ "0":{ "proportion":0.2655037162058198, "rate":0.2749303122566129 }, "1":{ "proportion":0.6321791898264187, "rate":0.9740711294478059 }, "2":{ "proportion":0.1023170939677615, "rate":3.041695877803997 } }, "Test":{ "0":{ "omega":0, "proportion":0.386646389823596 }, "1":{ "omega":0.9964438830494696, "proportion":0 }, "2":{ "omega":1.876622752045829, "proportion":0.613353610176404 } } }, "display order":2, "estimated parameters":40 } }, "input":{ "file name":"/tmp/tmpfqvtss8b/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)" } }, "test results":{ "LRT":10.17667489929045, "p-value":0.003084133210483175 }, "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":70 }, "Overall":{ "order":0, "timer":451 }, "Preliminary model fitting":{ "order":1, "timer":10 }, "Unconstrained BUSTED model fitting":{ "order":2, "timer":370 } } }