M1a

Usage

M1a(submodel: Double -> CTMC<Codons<a>>, omega0: Double, p0: Double) → DiscreteDist<CTMC<Codons<a>>>

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)|

omega0:

The omega value for conserved sites

Default: ~Uniform(0,1)

p0:

The fraction of conserved sites

Default: ~Uniform(0,1)

Description

A mixture of conserved and neutral sites. The conserved sites have frequency p0 and omega=omega0.

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.

The M1a model modifies the M1 model to avoid forcing the conserved omega to 0.

Examples

|w:GY94(omega=w,pi=F1x4)| +> M1a
|w:MG94(omega=w)| +> M1a
|w:FMutSel0(omega=w)| +> M1a

Citation

Wong, Wendy S. W.; Yang, Ziheng; Goldman, Nick; Nielsen, Rasmus (2004). Accuracy and Power of Statistical Methods for Detecting Adaptive Evolution in Protein Coding Sequences and for Identifying Positively Selected Sites. Genetics 168(2): 1041--1051. DOI: 10.1534/genetics.104.031153

See also

M2a, M2a_test, GTR, MNM, MutSelAA, dNdS