MutSelAA — Mutation-selection model with fitness values for amino-acids

Usage

MutSelAA(submodel: CTMC<Codons<a>>, ss: Map<String,Double>, a: Codons<a>) → CTMC<Codons<a>>

Type constraints: Nucleotides<a>

Aliases: mut_sel0

Arguments

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

submodel:

Model of neutral mutation

ss:

Scaled selection coefficients (2Ns)

Default: ~IIDOn(letters(getAminoAcids(a)), Laplace(0,1))

a:

The alphabet

Default: The alphabet in the current context

Original default expressions
ss 
~IIDOn(letters(getAminoAcids(@a)), Laplace(0,1))
a 
get_state(alphabet)

Description

Stationary inputs produce stationary models, whether reversible or not.

Non-equilibrium inputs retain their root frequencies.

Examples

GTR +> x3 +> dNdS +> MutSelAA

Citation

Yang, Ziheng; Nielsen, Rasmus (2008). Mutation-Selection Models of Codon Substitution and Their Use to Estimate Selective Strengths on Codon Usage. Molecular Biology and Evolution 25(3): 568--579. DOI: 10.1093/molbev/msm284

See also

MutSel, FMutSel