MG94 — The Muse & Gaut (1994) model of
dN/dS.
Usage
MG94(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.
-
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 MG94 model describes codon frequencies in terms of 4 nucleotide frequencies. It is thus similar to the GY94+F1x4 model where codon frequencies are constructed from 4 nucleotide frequencies. However, in the MG94 model rates from codon i to codon j only depend on the frequency of the affected nucleotide, and not on the frequencies of its neighbors.
The original MG94 model did not account for different rates in
transitions and transversions. See the MG94K model that is
extended to account for a ts/tv rate ratio, and the `MG94_ext model that
is extended to use an arbitrary nucleotide rate matrix.
The MG94 model is equivalent to the following models:
F81 +> x3 +> dNdS
MG94K[kappa=1]
MG94_ext(F81)
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