BranchSiteMixture

Usage

BranchSiteMixture(submodel: DiscreteDist<CTMC<a>>) → CTMC<a>

Arguments

submodel:

The model as a function of dN/dS

Description

Approximate a markov-modulated model by randomly choosing the rate matrix for each (branch,site) pair from the distribution of rate matrices.
The transition matrix P for each branch is the weighted average of the transition matrices P[i] computed from the mixture components.

Examples

|w: GTR +> x3 +> dNdS(w)| +> M3 +> BranchSiteMixture                       // = BUSTED
|w: GTR +> x3 +> dNdS(w)| +> M3 +> BranchSiteMixture +> ASRV.Gamma(n=3)   // = BUSTED-S

Citation

Murrell, Ben; Weaver, Steven; Smith, Martin D.; Wertheim, Joel O.; Murrell, Sasha; Aylward, Anthony; Eren, Kemal; Pollner, Tristan; Martin, Darren P.; Smith, Davey M.; Scheffler, Konrad; Kosakovsky Pond, Sergei L. (2015). Gene-Wide Identification of Episodic Selection. Mol. Biol. Evol. 32(5): 1365--1371. Article

See also

BUSTED, BUSTED_S