hyphy_meme: test-data/busted-out1.json comparison

comparison 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

comparison

equal deleted inserted replaced

-:7b3f9c78cf6d
+:d02c8e6f7f2a
 {
+"Evidence Ratios":{
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 "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. 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.",
+"authors":"Sergei L Kosakovsky Pond",
-"version":"1.2",
 "citation":"*Gene-wide identification of episodic selection*, Mol Biol Evol. 32(5):1365-71",
-"authors":"Sergei L Kosakovsky Pond",
 "contact":"spond@temple.edu",
-"requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})"
+"info":"BUSTED (branch-site unrestricted statistical test of episodic diversification) uses a random effects branch-site model fitted \njointly to all or a subset of tree branches in order to test for alignment-wide evidence of episodic diversifying selection. \nAssuming there is evidence of positive selection (i.e. there is an omega > 1),  BUSTED will also perform a quick evidence-ratio \nstyle analysis to 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,
+"branch attributes":{
+"0":{
+"Baboon":{
+"MG94xREV with separate rates for branch sets":0.001771850913718116,
+"Nucleotide GTR":0.00167976779100812,
+"constrained":0.0005055252388761481,
+"original name":"Baboon",
+"unconstrained":0.0005398732671668005
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-"p-value":1.893429857346973e-10
 }
 }

Mercurial > repos > iuc > hyphy_meme

comparison test-data/busted-out1.json @ 1:d02c8e6f7f2a draft