M3 — The M3 model

Usage

M3(submodel: Double -> CTMC<Codons<a>>, omegaDist: DiscreteDist<Double>, n: Int) → DiscreteDist<CTMC<Codons<a>>>

Arguments

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

submodel:

Codon model as a function of omega

Default: |w:GTR +> MNM +> MutSelAA +> dNdS(omega=w)|

omegaDist:

The omega values

Default: ~DirichletMixture(Uniform(0,1), 2, n)

n:

The number of omega categories, if not specified

Default: 4

Original default expressions
omegaDist 
~DirichletMixture(Uniform(0,1), 2, @n)

Description

A mixture of site categories with different omega values; by default these lie between zero and one.

The default background uses GTR, MNM, and MutSelAA. Here omega scales nonsynonymous rates after accounting for amino-acid fitnesses. Thus omega=1 retains these fitness effects; neutrality and positive selection are assessed relative to this background.

Examples

|w:GY94(omega=w,pi=F1x4)| +> M3
|w:MG94(omega=w)| +> M3
|w:FMutSel0(omega=w)| +> M3

Citation

Yang, Ziheng; Nielsen, Rasmus; Goldman, Nick; Pederson, Anne-Mette Krabbe (2000). Codon-Substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites. Genetics 155(1): 431--449. Article

See also

M3_test, GTR, MNM, MutSelAA, dNdS