Covarion.Galtier01 — The Galtier (2001) Covarion Model

Usage

Covarion.Galtier01(submodel: DiscreteDist<CTMC<a>>, nu: Double, pi: Double) → DiscreteDist<CTMC<a>>

Arguments

A default beginning with ~ specifies a prior distribution.

submodel:

The base mixture model

nu:

Rate of class-switching

Default: ~Exponential(0.1)

pi:

Fraction of sites undergoing class-switching

Default: ~Uniform(0,1)

Description

The Galtier covarion model implements switching between classes at a rate nu.

Examples

GTR +> ASRV.Gamma +> Covarion.Galtier01
GTR +> ASRV.Free +> Covarion.Galtier01

Citation

Galtier, Nicolas (2001). Maximum-likelihood phylogenetic analysis under a covarion-like model. Molecular Biology and Evolution 18(5): 866--873. DOI: 10.1093/oxfordjournals.molbev.a003868

See also

MarkovModulate