FMutSel
Usage
FMutSel(submodel: CTMC<a>, omega: Double, ss: Map<String,Double>, a: Codons<a>) → CTMC<Codons<a>>
Arguments
Underlined names in default expressions refer to other arguments. A
default beginning with ~ specifies a prior
distribution.
-
submodel: -
Model of neutral nucleotide substitution
-
Default:
GTR -
omega: -
Excess dN/dS
-
Default:
~LogNormal(0,1) -
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
With its default nucleotide model, FMutSel is equivalent to GTR +> x3 +> MutSel +> dNdS.
Stationary nucleotide inputs produce stationary codon models, whether reversible or not.
For non-equilibrium inputs, codon root frequencies are calculated from the nucleotide root frequencies; fitnesses and omega do not change them.
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