Mercurial > repos > iuc > hyphy_meme
diff test-data/busted-out1.json @ 1:d02c8e6f7f2a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
| author | iuc |
|---|---|
| date | Thu, 13 Feb 2020 15:03:27 -0500 |
| parents | 7b3f9c78cf6d |
| children | e0763df98352 |
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--- a/test-data/busted-out1.json Wed Aug 21 12:26:38 2019 -0400 +++ b/test-data/busted-out1.json Thu Feb 13 15:03:27 2020 -0500 @@ -1,361 +1,394 @@ { - "analysis":{ - "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. 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explore 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, - "fits":{ - "Nucleotide GTR":{ - "Log Likelihood":-3531.963798530155, - "estimated parameters":24, - "AIC-c":7112.142458295762, - "Equilibrium frequencies":[ - [0.3563279857397504], - [0.1837789661319073], - [0.2402852049910873], - [0.2196078431372549] - ], - "Rate Distributions":{ - "Substitution rate from nucleotide A to nucleotide C":0.5474490057204714, - "Substitution rate from nucleotide A to nucleotide G":1, - "Substitution rate from nucleotide A to nucleotide T":0.2645352969683238, - "Substitution rate from nucleotide C to nucleotide G":0.4863078374555331, - "Substitution rate from nucleotide C to nucleotide T":1.018028772244997, - "Substitution rate from nucleotide G to nucleotide T":0.3025951149895378 - }, - "display order":0 - }, - "MG94xREV 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