M2a
Usage
M2a(submodel: Double
-> CTMC<Codons<a>>, omega0: Double, p0: Double, posP: Double, posW: 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 among non-positively selected sites
-
Default:
~Uniform(0,1) -
posP: -
The fraction of positively selected sites
-
Default:
~Beta(1,10) -
posW: -
The omega value for positively selected sites
-
Default:
~LogGamma(4,0.25)
Description
A mixture of conserved, neutral, and positively-selected sites. The conserved sites have omega=omega0 and the positively-selected sites have omega=posW. In this parameterization of the M2a model, p0 is the probability of being conserved conditional on not being positively selected.
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 M2a model modifies the M2 model to avoid forcing the conserved omega to 0.
Examples
|w:GY94(omega=w,pi=F1x4)| +> M2a|w:MG94(omega=w)| +> M2a|w:FMutSel0(omega=w)| +> M2aCitation
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