Mercurial > repos > iuc > drhip
diff test-data/BUSTED/gene1.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/gene1.json Thu Dec 04 15:05:26 2025 +0000 @@ -0,0 +1,713 @@ +{ + "Evidence Ratios":{ + }, + "Site Log Likelihood":{ + "unconstrained": [ +[-3.290019315059098, -4.175663627535955, -4.175663627535955, -4.173115241795732, -9.238614141422939, -6.201388047751721, -3.588161705747214, -3.846065275733122, -11.6279127051655, -4.374967447338868, -4.667251719415955, -5.369450552211644, -4.609545779703736, -4.521369648345189, -3.290019315059098, -4.472687242532417, -3.396709886941963, -5.214702609387182, -4.561720576655006, -3.577740971164724, -4.175663627535955, -5.214702609387182, -4.169795185009985, -4.22785259313233, -4.775958986232662, -11.23524464752527, -14.05898845363783, -4.364741485582735, -4.188622564988608, -4.561720576655006, -3.588161705747214, -3.577740971164724, -4.609545779703736, -4.22785259313233, -10.80905338405208, -4.290623032758742, -4.188622564988608, -9.102696648764709, -10.15065862754325, 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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":{ + "Node3":{ + "MG94xREV with separate rates for branch sets":0.007049012269592678, + "Nucleotide GTR":0.007289662052004695, + "Posterior prob omega class": [ +[0], + [0.9353670953035417], + [0.06461204144565623], + [2.086325080203871e-05] + ], + "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], + [0.9151977400221446, 0.9149330883022148, 0.9149330883022148, 0.9148696121842339, 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