Mercurial > repos > iuc > hyphy_meme
view test-data/absrel-out1.json @ 29:d0f087aae1a3 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ec5db8349483b2cd46f9da23abe6cefcf65bc714"
author | iuc |
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date | Sat, 03 Jul 2021 09:04:24 +0000 (2021-07-03) |
parents | 546f2f99b820 |
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{ "analysis":{ "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group", "citation":"Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection (2015). Mol Biol Evol 32 (5): 1342-1353. v2.2 adds support for multiple-hit models", "contact":"spond@temple.edu", "info":"aBSREL (Adaptive branch-site random effects likelihood)\n uses an adaptive random effects branch-site model framework\n to test whether each branch has evolved under positive selection,\n using a procedure which infers an optimal number of rate categories per branch.", "requirements":"in-frame codon alignment and a phylogenetic tree", "version":"2.2" }, "branch attributes":{ "0":{ "Baboon":{ "Baseline MG94xREV":0.001816807585564731, "Baseline MG94xREV omega ratio":0, "Corrected P-value":1, "Full adaptive model":0.001810407118394509, "LRT":0, "Nucleotide GTR":0.001678881906620672, "Rate Distributions": [ [0, 1] ], "Rate classes":1, "Uncorrected P-value":1, "original name":"Baboon", "rate at which 2 nucleotides are changed instantly within a single codon":0 }, "Cat":{ "Baseline MG94xREV":0.2286001363527903, "Baseline MG94xREV omega ratio":1.403298474422089, "Corrected P-value":1, "Full adaptive model":0.1219386838393392, "LRT":1.644967676056694, "Nucleotide GTR":0.265904547400163, "Rate Distributions": [ [0.2130519766306851, 0.6352283641519592], [2.628217450705319, 0.3647716358480408] ], "Rate classes":2, "Uncorrected P-value":0.171730764045231, "original name":"Cat", "rate at which 2 nucleotides are changed instantly within a single codon":0 }, "Chimp":{ "Baseline MG94xREV":0.001840311209746262, "Baseline MG94xREV omega ratio":10000000000, "Corrected P-value":1, "Full adaptive model":0.001841979303044237, "LRT":0.6159123786974305, "Nucleotide GTR":0.001816713800925801, "Rate Distributions": [ [10000000000, 1] ], "Rate classes":1, "Uncorrected P-value":0.3069983227523322, "original name":"Chimp", "rate at which 2 nucleotides are changed instantly within a single codon":0 }, "Cow":{ "Baseline MG94xREV":0.2070244948790512, "Baseline MG94xREV omega ratio":2.153434974462683, "Corrected P-value":0.5006146299996015, "Full adaptive model":0.1241125417707662, "LRT":4.898194538953248, "Nucleotide GTR":0.2481512612523618, "Rate Distributions": [ [0, 0.52318726440949], [2.444056517734385, 0.47681273559051] ], "Rate classes":2, "Uncorrected P-value":0.03128841437497509, "original name":"Cow", "rate at which 2 nucleotides are changed instantly within a single codon":0 }, "Horse":{ "Baseline MG94xREV":0.190365915457708, "Baseline MG94xREV omega ratio":1.182933895494305, "Corrected P-value":1, "Full adaptive model":0.0869489794025302, "LRT":2.047309801283518, "Nucleotide GTR":0.2090927256979082, "Rate Distributions": [ [0, 0.5397658078247131], [1.633257246666139, 0.4602341921752869] ], "Rate classes":2, "Uncorrected P-value":0.1382789032066179, "original name":"Horse", "rate at which 2 nucleotides are changed instantly within a single codon":0 }, "Human":{ "Baseline MG94xREV":0, "Baseline MG94xREV omega ratio":1, "Corrected P-value":1, "Full adaptive model":0, "LRT":0, "Nucleotide GTR":0, "Rate Distributions": [ [1, 1] ], "Rate classes":1, "Uncorrected P-value":1, "original name":"Human", "rate at which 2 nucleotides are changed instantly within a single codon":0.0006106118725184574 }, "Mouse":{ "Baseline MG94xREV":0.1083167307250788, "Baseline MG94xREV omega ratio":0.5108576904540283, "Corrected P-value":1, "Full adaptive model":0.1078010043714489, "LRT":0, "Nucleotide GTR":0.1181001275359051, "Rate Distributions": [ [0.5087375113796073, 1] ], "Rate classes":1, "Uncorrected P-value":1, "original name":"Mouse", "rate at which 2 nucleotides are changed instantly within a single codon":0.4244832903005548 }, "Node1":{ "Baseline MG94xREV":0.2542393300501047, "Baseline MG94xREV omega ratio":0.2997498382776075, "Corrected P-value":1, "Full adaptive model":0.2550466752020236, "LRT":0, "Nucleotide GTR":0.2767426965701868, "Rate Distributions": [ [0.2932817609633239, 1] ], "Rate classes":1, "Uncorrected P-value":1, "rate at which 2 nucleotides are changed instantly within a single codon":0.9114373463003921 }, "Node12":{ "Baseline MG94xREV":0.01400815185374474, "Baseline MG94xREV omega ratio":0.2754467062829232, "Corrected P-value":1, "Full adaptive model":0.01437973904273591, "LRT":0, "Nucleotide GTR":0.01784721909304638, "Rate Distributions": [ [0.3037614070859027, 1] ], "Rate classes":1, "Uncorrected P-value":1, "rate at which 2 nucleotides are changed instantly within a single codon":0.5084909616267814 }, "Node2":{ "Baseline MG94xREV":0.0400106272595141, "Baseline MG94xREV omega ratio":0.116408812566168, "Corrected P-value":1, "Full adaptive model":0.03991940069030483, "LRT":0, "Nucleotide GTR":0.06613304839358287, "Rate Distributions": [ [0.1193993042178124, 1] ], "Rate classes":1, "Uncorrected P-value":1, "rate at which 2 nucleotides are changed instantly within a single codon":9.28646275825122 }, "Node3":{ "Baseline MG94xREV":0.08548068002443369, "Baseline MG94xREV omega ratio":1.293385437932658, "Corrected P-value":1, "Full adaptive model":0.08590119038008139, 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"Baseline MG94xREV":0.003671939837747083, "Baseline MG94xREV omega ratio":10000000000, "Corrected P-value":1, "Full adaptive model":0.003675047654636179, "LRT":1.165062770327495, "Nucleotide GTR":0.003777016173741061, "Rate Distributions": [ [10000000000, 1] ], "Rate classes":1, "Uncorrected P-value":0.2236284592802686, "original name":"RhMonkey", "rate at which 2 nucleotides are changed instantly within a single codon":0 } }, "attributes":{ "Baseline MG94xREV":{ "attribute type":"branch length", "display order":1 }, "Baseline MG94xREV omega ratio":{ "attribute type":"branch label", "display order":1 }, "Corrected P-value":{ "attribute type":"branch label", "display order":6 }, "Full adaptive model":{ "attribute type":"branch length", "display order":2 }, "LRT":{ "attribute type":"branch label", "display order":4 }, "Nucleotide GTR":{ "attribute type":"branch length", "display order":0 }, "Rate Distributions":{ "attribute type":"branch label", "display order":3 }, "Rate classes":{ "attribute type":"branch label", "display order":2 }, "Uncorrected P-value":{ "attribute type":"branch label", "display order":5 }, "original name":{ "attribute type":"node label", "display order":-1 }, "rate at which 2 nucleotides are changed instantly within a single codon":{ "attribute type":"branch label", "display order":7 } } }, "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":"absrel.filter.default" } }, "fits":{ "Baseline MG94xREV":{ "AIC-c":6983.763305606333, "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], [0.006267234867003878], [0.005260551308914496], [0.006459711194459957], [0.005277194922783805], [0.006554399593040238], [0.005501589790395056], 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"Mean":666666667.5119981, "Median":1 } }, "display order":1, "estimated parameters":62 }, "Full adaptive model":{ "AIC-c":6972.859938351839, "Log Likelihood":-3415.824749853321, "Rate Distributions":{ }, "display order":2, "estimated parameters":68 }, "Nucleotide GTR":{ "AIC-c":7112.857317645923, "Equilibrium frequencies": [ [0.3592490842490842], [0.181959706959707], [0.240018315018315], [0.2187728937728937] ], "Log Likelihood":-3532.321228205235, "Rate Distributions":{ "Substitution rate from nucleotide A to nucleotide C":0.5498703043473002, "Substitution rate from nucleotide A to nucleotide G":1, "Substitution rate from nucleotide A to nucleotide T":0.2646979624678532, "Substitution rate from nucleotide C to nucleotide G":0.4921328068285813, "Substitution rate from nucleotide C to nucleotide T":1.028960084526602, "Substitution rate from nucleotide G to nucleotide T":0.3044365000595399 }, "display order":0, "estimated parameters":24 } }, "input":{ "file name":"/tmp/tmpx_42i6f0/job_working_directory/000/6/working/./absrel_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":{ "P-value threshold":0.05, "positive test results":0, "tested":16 }, "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":{ "Baseline model fitting":{ "order":2, "timer":17 }, "Complexity analysis":{ "order":3, "timer":110 }, "Full adaptive model fitting":{ "order":4, "timer":20 }, "Overall":{ "order":0, "timer":259 }, "Preliminary model fitting":{ "order":1, "timer":0 }, "Testing for selection":{ "order":5, "timer":112 } } }