Covarion.Wang07 — The WSSR (2007) Covarion Model
Usage
Covarion.Wang07(submodel: DiscreteDist<CTMC<a>>,
r: Double, pi1: Double, nu: Double, pi: Double) → DiscreteDist<CTMC<a>>
Arguments
A default beginning with ~ specifies a prior
distribution.
-
submodel: -
The base mixture model
-
r: -
s01 + s10
-
Default:
~Gamma(2,1/4) -
pi1: -
Fraction of time spent in the ON state
-
Default:
~Beta(2,2) -
nu: -
Rate of class-switching
-
Default:
~Exponential(0.1) -
pi: -
Fraction of sites undergoing class-switching
-
Default:
~Uniform(0,1)
Description
The WSSR covarion model implements both switching between ON/OFF states, and switching between classes.
Examples
GTR +> ASRV.Gamma +> Covarion.Wang07GTR +> ASRV.Free +> Covarion.Wang07Citation
Wang, Huai-Chun; Spenser, Matthew; Susko, Edward; Roger, Andrew J (2007). Testing for Covarion-like Evolution in Protein Sequences. Molecular Biology and Evolution 24(1): 294--305. DOI: 10.1093/molbev/msl155