Mercurial > repos > iuc > hyphy_absrel
diff test-data/absrel-out1.json @ 16:4cc4dbca2f02 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 7868bb22136a87ff5120042ce90bc6be87d57d80"
| author | iuc |
|---|---|
| date | Fri, 18 Sep 2020 21:10:47 +0000 |
| parents | 419cd817299c |
| children |
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--- a/test-data/absrel-out1.json Fri Aug 21 15:24:17 2020 -0400 +++ b/test-data/absrel-out1.json Fri Sep 18 21:10:47 2020 +0000 @@ -1,424 +1,253 @@ { "analysis":{ - "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.", - "version":"2.0", - "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", "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", - "requirements":"in-frame codon alignment and a phylogenetic tree" - }, - "input":{ - "file name":"/tmp/tmpCAMqUO/job_working_directory/002/2602/working/absrel_input.fa", - "number of sequences":10, - "number of sites":187, - "partition count":1, - "trees":{ - "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.085099,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":-3531.96369518556, - "estimated parameters":24, - "AIC-c":7112.577796875186, - "Equilibrium frequencies":[ - [0.3563279857397504], - [0.1837789661319073], - [0.2402852049910873], - [0.2196078431372549] - ], - "Rate Distributions":{ - "Substitution rate from nucleotide A to nucleotide C":0.5474707834424497, - "Substitution rate from nucleotide A to nucleotide G":1, - "Substitution rate from nucleotide A to nucleotide T":0.2645731370379643, - "Substitution rate from nucleotide C to nucleotide G":0.4867482826410435, - "Substitution rate from nucleotide C to nucleotide T":1.018295973581558, - "Substitution rate from nucleotide G to nucleotide T":0.3026112531229544 - }, - "display order":0 - }, - "Baseline MG94xREV":{ - "Log Likelihood":-3450.669934819203, - "estimated parameters":46, - "AIC-c":6995.711784065174, - "Equilibrium frequencies":[ - [0.04787662253946073], - [0.03913388100305117], - [0.04844580322128512], - [0.0407178971288476], - [0.01817959331488358], - [0.01485982100934833], - [0.01839572120297191], - [0.01546129971531724], - [0.0190238172858878], - [0.01554988139098808], - [0.01924998172104109], - [0.01617929156565557], - [0.02798385246472159], - [0.02287372613761008], - [0.02831653817605838], - [0.02379958245776909], - [0.01680670574479072], - [0.01373763619452979], - 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"Horse":"test", - "Cat":"test", - "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":"absrel.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] - ] - } + "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":{ - "Human":{ - "original name":"Human", - "Nucleotide GTR":0, - "Baseline MG94xREV":0, - "Baseline MG94xREV omega ratio":1, - "Rate classes":1, - "Full adaptive model":0, - "Rate Distributions":[ - [1, 1] - ], + "Baboon":{ + "Baseline MG94xREV":0.001816807585564731, + "Baseline MG94xREV omega ratio":0, + "Corrected P-value":1, + "Full adaptive model":0.001810407118394509, "LRT":0, - "Uncorrected P-value":1, - "Corrected P-value":1 - }, - 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