Mercurial > repos > iuc > drhip
diff test-data/BUSTED/gene2.json @ 0:dd2d60b55e0d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drhip commit 15c654c3d27df68a47483031961ace7f5b8d998d
| author | iuc |
|---|---|
| date | Thu, 04 Dec 2025 15:05:26 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/BUSTED/gene2.json Thu Dec 04 15:05:26 2025 +0000 @@ -0,0 +1,695 @@ +{ + "Evidence Ratios":{ + }, + "Site Log Likelihood":{ + "unconstrained": [ +[-3.279395301242991, -4.158105567096131, -4.158105567096131, -4.166638466034495, -9.154212641369053, -6.1646364993799, -3.571664296153773, -3.824743577643191, -11.53832927288458, -4.367126880116822, -4.649201391250461, -5.362307946868293, -4.590683278931873, -4.520169530632763, -3.279395301242991, -4.478009948274525, -3.38374975421236, -5.200806733026117, -4.539965496430686, -3.56153094378479, -4.158105567096131, -5.200806733026117, -4.15773284428875, -4.20405974806271, -4.771500568226211, -11.13805742664432, -14.13307082606694, -4.354646049384101, -4.178467862588951, -4.539965496430686, -3.571664296153773, -3.56153094378479, -4.590683278931873, -4.20405974806271, -10.84017869555231, -4.273530749914073, -4.178467862588951, -9.045592451013922, -4.20405974806271, -5.091559959583829, 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identification of episodic selection*, Mol Biol Evol. 32(5):1365-71, *Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril*, Mol Biol Evol. 37(8):2430-2439", + "contact":"spond@temple.edu", + "info":"BUSTED (branch-site unrestricted statistical test of episodic diversification) uses a random effects branch-site model fitted jointly to all or a subset of tree branches in order to test for alignment-wide evidence of episodic diversifying selection. Assuming there is evidence of positive selection (i.e. there is an omega > 1), BUSTED will also perform a quick evidence-ratio style analysis to explore which individual sites may have been subject to selection. v2.0 adds support for synonymous rate variation, and relaxes the test statistic to 0.5 (chi^2_0 + chi^2_2).\n \nVersion 2.1 adds a grid search for the initial starting point.\n\nVersion 2.2 changes the grid search to LHC, and adds an initial search phase to use adaptive Nedler-Mead. \n\nVersion 3.0 implements the option for branch-site variation in synonymous substitution rates. \n\nVersion 3.1 adds HMM auto-correlation option for SRV, and binds SRV distributions for multiple branch sets.\n\nVersion 4.0 adds support for multiple hits (MH), ancestral state reconstruction saved to JSON, and profiling of branch-site level support for selection / multiple hits.\n\nVersion 4.2 adds calculation of MH-attributable fractions of substitutions.\n\nVersion 4.5 adds an 'error absorption' component \n\nVersion 4.6 adds support for MSS-type models\n", + "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})", + "settings":{ + "error-sink":1, + "mss":"No", + "multiple-hit":"None", + "srv":"Yes" + }, + "version":"4.6" + }, + "background":1, + "branch attributes":{ + "0":{ + "Node2":{ + "MG94xREV with separate rates for branch sets":0.01556490736651599, + "Nucleotide GTR":0.01391650578382423, + "Posterior prob omega class": [ +[0], + [0.1290568055362266], + [0.8709431507439804], + [4.371979290886899e-08] + ], + "Posterior prob omega class by site": [ +[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], + [0.1011376447591334, 0.1009434234318572, 0.1009434234318572, 0.1008948518096908, 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