M1a
Usage
M1a(submodel: Double
-> CTMC<Codons<a>>, omega0: Double, p0: 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)| -
omega0: -
The dN/dS value for conserved sites
-
Default:
~Uniform(0,1) -
p0: -
The fraction of conserved sites
-
Default:
~Uniform(0,1)
Description
A mixture of conserved and neutral sites. The conserved sites have frequency p0 and dN/dS=omega0.
The M1a model modifies the M1 model to avoid forcing the conserved dN/dS to 0.
Examples
|w:GY94(omega=w,pi=F1x4)| +> M1a|w:MG94(omega=w)| +> M1a|w:FMutSel0(omega=w)| +> M1aCitation
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