MG94_ext — An extended version of the Muse & Gaut (1994) model of codon substitution.

Usage

MG94_ext(nucModel: CTMC<n>, omega: Double, a: Codons<n>) → CTMC<Codons<n>>

Type constraints: Nucleotides<n>

Arguments

A default beginning with ~ specifies a prior distribution.

nucModel:

Nucleotide substitution rate matrix

omega:

Relative rate of non-synonymous changes relative to synonymous changes

Default: ~LogNormal(0,1)

a:

The alphabet

Default: The alphabet in the current context

Original default expressions
a 
get_state(alphabet)

Description

This is a version of the MG94 model that has been extended to use a user-supplied rate matrix nucModel on nucleotides. The original MG94 model is equivalent to MG94_ext(F81).

Examples

MG94_ext(HKY85(kappa=2),omega=2)
MG94_ext(GTR)

Citation

Muse, Spencer V; Gaut, Brandon S (1994). A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome.. Molecular biology and evolution 11(5): 715--724. Article

See also

MG94