GY94 — The Goldman & Yang (1994) model of dN/dS

Usage

GY94(kappa: Double, omega: Double, pi: Map<String,Double>, a: Codons<n>) → CTMC<Codons<n>>

Type constraints: Nucleotides<n>

Aliases: m0

Arguments

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

kappa:

Transition/transversion ratio

Default: ~LogNormal(log(2),0.25)

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)

Examples

GY94(kappa=2,omega=2)
GY94(pi=F1x4)
GY94(pi=F3x4)

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_ext, MG94