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Tweak help for busted and busted_s.
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bredelings committed Dec 31, 2024
1 parent f5bbe21 commit 3392b0b
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4 changes: 2 additions & 2 deletions bindings/models/busted.json
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Expand Up @@ -41,7 +41,7 @@
"description": "The number of conserved omega categories, if not specified"
}
],
"description": "This model performs a Bayesian test of positive selection using the BUSTED model. The BUSTED model constructs a weighted list of (n+1) dN/dS values and constructs rate matrices from them. The first n rate matrices are conserved, and the last rate matrix is positive selected with weight posP and dNdS=posW. Instead switching between these rate matrices using a covarion process, the BUSTED model simply lets each (branch,site) pair choose a rate matrix from the mixture.\nThe test for positive selection compares the unrestricted BUSTED model to a restricted version with posW=1. The posterior probability that posSelection=1 is posterior probability for positive selection.\nAll branches are treated as foreground branches.",
"description": "A Bayesian test of positive selection using the BUSTED model. The BUSTED model constructs a weighted list of (n+1) dN/dS values and constructs rate matrices from them. The first n rate matrices are conserved, and the last rate matrix is positive selected with weight posP and dNdS=posW. Instead switching between these rate matrices using a covarion process, the BUSTED model simply lets each (branch,site) pair choose a rate matrix from the mixture.\nThe test for positive selection compares the unrestricted BUSTED model to a restricted version with posW=1. The posterior probability that posSelection=1 is posterior probability for positive selection.\nAll branches are treated as foreground branches.",
"extract": "all",
"citation": {"type": "article",
"title": "Gene-Wide Identification of Episodic Selection",
Expand All @@ -66,5 +66,5 @@
"busted +> Rates.free",
"|w: gtr +> mnm +> dNdS(omega=w)| +> busted // with multi-nucleotide mutations",
"|w: gtr +> x3 +> dNdS(omega=w) +> mut_sel| +> busted // with mutation-selection-balance"],
"see": ["busted_s"]
"see": ["branch_site_mixture","busted_s"]
}
4 changes: 2 additions & 2 deletions bindings/models/busted_s.json
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Expand Up @@ -53,7 +53,7 @@
"description": "The number of conserved omega categories, if not specified"
}
],
"description":"This model performs a Bayesian test of positive selection using the BUSTED-S model. The BUSTED-S model handles synonymous rate variation by adding Gamma-distributed across-site rate variation (ASRV) to the BUSTED model using n=3 bins.",
"description":"A Bayesian test of positive selection using the BUSTED-S model. The BUSTED-S model handles synonymous rate variation by adding Gamma-distributed across-site rate variation (ASRV) to the BUSTED model using n=3 bins.",
"extract": "all",
"citation": {"type": "article",
"title": "Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril",
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"journal": {"name": "Mol. Biol. Evol.", "volume": "37", "number": "8", "pages": "2430--2439"},
"link": [{"url":"https://doi.org/10.1093/molbev/msaa037"}]
},
"see": ["busted"],
"see": ["branch_site_mixture", "busted"],
"examples": ["|w: tn93 +> x3 +> dNdS(omega=w)| +> busted_s",
"|w: tn93 +> mnm +> dNdS(omega=w)| +> busted_s"]
}

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