MutSel — Fitness modifier with state-specific
fitnesses
Usage
MutSel(submodel: CTMC<a>, ss: Map<String,Double>, a: a)
→ CTMC<a>
Arguments
Underlined names in default expressions refer to other arguments. A
default beginning with ~ specifies a prior
distribution.
-
submodel: -
Model of neutral mutation
-
a: -
The alphabet
-
Default: The alphabet in the current context
Original default expressions
-
ss -
~IIDOn(letters(@a), Laplace(0,1)) -
a -
get_state(alphabet)
Description
Modify an input mutation rate matrix using a fitness for each state (each codon for a codon alphabet). This is a model component, not a complete codon model. The construction GTR +> x3 +> MutSel +> dNdS gives FMutSel with default arguments. Replacing x3 with MNM extends the mutation model to include multinucleotide changes.
Stationary inputs produce stationary models, whether reversible or not.
Non-equilibrium inputs retain their root frequencies.
Examples
GTR +> x3 +> MutSel +> dNdSGTR +> x2 +> MutSelCitation
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