M8 — Beta-distributed omega with an additional
positively selected category
Usage
M8(submodel: Double
-> CTMC<Codons<a>>, n: Int, mu: Double, v: 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)| -
n: -
Number of categories approximating the Beta distribution
-
Default:
10 -
mu: -
The mean of the Beta distribution
-
Default:
~Uniform(0,1) -
v: -
The normalized Beta variance Var(omega)/(mu*(1-mu)); 0 < v < 1
-
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
M8 combines an M7 component of weight 1-posP with an additional category of weight posP and omega=posW. The default prior restricts posW to values greater than 1 (positive selection).
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 Beta component uses Gauss-Jacobi quadrature with generally unequal category weights. There are n+1 categories in total.
Citation
Yang, Ziheng; Nielsen, Rasmus; Goldman, Nick; Pedersen, Anne-Mette Krabbe (2000). Codon-Substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites. Genetics 155(1): 431--449. Article