M8
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: -
The model, as a function of dN/dS
-
Default:
|w:GY94(omega=w)| -
n: -
The number of Gauss-Jacobi quadrature categories for the Beta component
-
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 dN/dS value for positively selected sites
-
Default:
~LogGamma(4,0.25)
Description
The M8 model is an M7 model with an additional category of positively-selected sites. The additional category of sites has proportion=posP and dN/dS=posW.
The Beta component uses Gauss-Jacobi quadrature with generally unequal category weights. The parameter n counts Beta categories, excluding any additional M8-family category.
The Beta-component mean mu and normalized variance v have independent Uniform(0,1) default priors.
Citation
Yang, Ziheng; Nielsen, Rasmus; Goldman, Nick; Pederson, Anne-Mette Krabbe (2000). Codon-Substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites. Genetics 155(1): 431--449. Article