Rev Language Reference

The Muse-Gaut (1994) codon model, extended with a transition/transversion rate ratio. A rate matrix on the 61 non-stop codons (in the standard genetic code). Rates between codons with more than one nucleotide change are equal to 0. In this model the rate Q(i,j) from i -> j is proportional to the frequency of nucleotide in codon j that changed. This differs from the Goldman-Yang (1994) model, where Q(i,j) is proportional to the frequency of the entire codon j. This version is an extension of the fnCodonMG94 model to add a transition/transversion rate ratio. This makes it more comparable to the Goldman-Yang (1994) model. Unlike the Goldman-Yang (1994) model, the Muse-Gaut (1994) model does not allow all the codon frequencies to vary independently.

kappa ~ dnLognormal(0,1)
omega ~ dnUniform(0,1)
pi ~ dnDirichlet( rep(2.0, 4) )
Q1 := fnCodonMG94K( kappa, omega, pi )

Q2 := fndNdS( omega, fnX3( fnHKY( kappa, pi) ) ) # MG94K = HKY + X3 + dNdS