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.
Usage
Arguments
| 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
Example
omega ~ dnUniform(0,1)
pi ~ dnDirichlet( rep(2.0, 4) )
Q1 := fnCodonMG94( omega, pi )
Q2 := fndNdS( omega, fnX3( fnF81(pi) ) ) # MG94 = F81 + X3 + dNdS
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