GY94_ext — An extended version of the Goldman & Yang (1994) model of dN/dS

Usage

GY94_ext(nucModel: ExchangeModel<n>, omega: Double, pi: Map<String,Double>, a: Codons<n>) → CTMC<Codons<n>>

Type constraints: Nucleotides<n>

Arguments

Underlined names in default expressions refer to other arguments. A default beginning with ~ specifies a prior distribution.

nucModel:

Symmetric exchange rates on nucleotides

omega:

Relative rate of non-synonymous changes relative to synonymous changes

Default: ~LogNormal(0,1)

pi:

Letter frequencies

Default: ~SymmetricDirichletOn(letters(a),1)

a:

The codon alphabet

Default: The alphabet in the current context

Original default expressions
pi 
~SymmetricDirichletOn(letters(@a),1)
a 
get_state(alphabet)

Description

This is a version of the GY94 model that has been extended to use user-supplied exchangabilty matrix nucModel on nucleotides. The original GY94 model distinguishes only between transitions and transversions, and is equivalent to GY94_ext(HKY85_sym).

Examples

GY94_ext(HKY85_sym(kappa=2),omega=2)
GY94_ext(GTR_sym,pi=F1x4)

Citation

Goldman, Nick; Yang, Ziheng (1994). A codon-based model of nucleotide substitution for protein-coding DNA sequences. Molecular biology and evolution 11(5): 725--736. Article

See also

GY94