Rev Language Reference
fnCodonGY94 - The Goldman-Yang (1994) codon rate matrix
The Goldman-Yang (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 codon j.
This means that the rate of change between low-frequency codons is lower than the rate
between high-frequency codons, even when the nucleotide change involved is the same.
In other words, the rate of change from nucleotide n1 -> n2 depends on its neighboring
nucleotides. This differs from the Muse-Gaut (1994) model, and is perhaps less realistic.
Unlike the Muse-Gaut (1994) model, the Goldman-Yang (1994) model can allow all the codon
frequencies to vary independently.
Usage
Arguments
| omega : | RealPos (pass by const reference) |
| The dN / dS rate ratio. | |
| kappa : | RealPos (pass by const reference) |
| The transition-transversion rate ratio. | |
| codonFrequencies : | Simplex (pass by const reference) |
| The stationary frequencies of the codons. |
Return Type
Example
kappa ~ dnLognormal(0,1)
omega ~ dnUniform(0,1)
pi61 ~ dnDirichlet( rep(2.0, 61) )
Q1 := fnCodonGY94( kappa, omega, pi61 )
pi1 ~ dnDirichlet( rep(2.0, 4) )
Q2 := fnCodonGY94( kappa, omega, fnF1x4(pi1) )
pi2 ~ dnDirichlet( rep(2.0, 4) )
pi3 ~ dnDirichlet( rep(2.0, 4) )
Q3 := fnCodonGY94( kappa, omega, fnF3x4(pi1, pi2, pi3) )
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