Full
model name: Muse-Gaut 1994 with independent rate variation.
Model type:
Codon.
Model
options:
The user specifies the number of rate classes for synonymous rates, and the number of rate classes for non-synonymous rates.
Independent
Parameters:
t - branch length, R- non-synonymous
to synonymous ratio, or to be more precise, the ratio
of mean non-syn to mean syn rate (shared by all branches),
alpha - the shape parameter for the unit mean gamma distribution
of synonymous rates (shared by all branches), beta - the shape parameter for the unit mean gamma distribution of synonymous rates (shared by all branches).
Rate Matrix
Entries:
Note: the rate matrix will have the same dimension
as the number of non-stop codons in the genetic code which is
being used be the analysis (61 for Universal Code).
c,d are distributed (independently)
as unit mean gammas, with shape parameters alpha and beta, respectively.
Example of a one-step change: ACC->ATC;
more than one step: ACC->CGC.
refers to the observed
frequency of the target nucleotide that is changed in transition
from i to j. (E.g. it is the frequency of T in
the example above).
Equilibrium
frequencies of codons:
Equilibrium frequency of codon ijk
is the product of observed frequencies of nucleotides
which compose the codon, normalized by a factor to account for
the presence of stop codons.
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