# 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

fnCodonGY94(RealPos omega, RealPos kappa, Simplex codonFrequencies)

### 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.

### 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) )