M8a
Usage
M8a(submodel: Double
-> CTMC<Codons<a>>, n: Int, mu: Double, v: Double, posP: 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 neutral sites
-
Default:
~Beta(1,10)
Description
The M8a model is an M7 model with an additional category of neutral sites. The additional category of sites has proportion posP.
The M8a model is also equivalent to M8(posW=1). That is, you get M8a by constraining posW to 1 in the M8 model. Therefore, the M8a model is nested within the M8 model.
The M8a model was created as an improved null hypothesis for use in a likelihood ratio test. (See M8a_test)
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
Swanson, Willie J.; Nielsen, Rasmus; Yang, Qiaofeng (2003). Pervasive Adaptive Evolution in Mammalian Fertilization Proteins. Molecular Biology and Evolution 20(1): 18--20. DOI: 10.1093/oxfordjournals.molbev.a004233