MG94K — The Muse & Gaut (1994) model of codon
substitution.
Usage
MG94K(kappa: Double, omega: Double, pi: Map<String,Double>, a: Codons<n>) → CTMC<Codons<n>>
Arguments
Underlined names in default expressions refer to other arguments. A
default beginning with ~ specifies a prior
distribution.
-
kappa: -
Transition/transversion ratio
-
Default:
~LogNormal(log(2),0.25) -
omega: -
Relative rate of non-synonymous changes relative to synonymous changes
-
Default:
~LogNormal(0,1) -
a: -
The alphabet
-
Default: The alphabet in the current context
Original default expressions
-
pi -
~SymmetricDirichletOn(letters(getNucleotides(@a)), 1.0) -
a -
get_state(alphabet)
Description
The MG94K model extends the MG94 model to account for different rates of transitions and transversions.
The MG94K model is equivalent to the following models:
HKY85 +> x3 +> dNdS
MG94_ext[HKY85]
Citation
Muse, Spencer V; Gaut, Brandon S (1994). A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome.. Molecular biology and evolution 11(5): 715--724. Article