Rev Language Reference

fnCodonMG94 - The Muse-Gaut (1994) codon rate matrix

The Muse-Gaut (1994) codon model. 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. Unlike the Goldman-Yang (1994) model, the Muse-Gaut (1994) model does not allow all the codon frequencies to vary independently.


fnCodonMG94(RealPos omega, Simplex baseFrequencies)


omega : RealPos (pass by const reference)
The dN / dS rate ratio.
baseFrequencies : Simplex (pass by const reference)
The stationary frequencies of the nucleotides.

Return Type


omega ~ dnUniform(0,1)
pi ~ dnDirichlet( rep(2.0, 4) )
Q1 := fnCodonMG94( omega, pi )

Q2 := fndNdS( omega, fnX3( fnF81(pi) ) ) # MG94 = F81 + X3 + dNdS

See Also