Rev Language Reference

fnF3x4 - The F3x4 codon frequency model

This treats codon frequencies as a product of independent nucleotide frequencies. Since stop codons are removed from the codon alphabet, frequencies are renormalized so that the frequencies of non-stop codons sum to 1.0.

Usage

fnF3x4(Simplex baseFrequencies1, Simplex baseFrequencies2, Simplex baseFrequencies3)

Arguments

baseFrequencies1 : Simplex (pass by const reference)
The stationary frequencies of the 1st nucleotide.
baseFrequencies2 : Simplex (pass by const reference)
The stationary frequencies of the 2nd nucleotide.
baseFrequencies3 : Simplex (pass by const reference)
The stationary frequencies of the 3rd nucleotide.

Return Type

Simplex

Example

kappa ~ dnLognormal(0,1)
omega ~ dnUniform(0,1)
pi1 ~ dnDirichlet( v(2.0, 2.0, 2.0, 2.0) )
pi2 ~ dnDirichlet( v(2.0, 2.0, 2.0, 2.0) )
pi3 ~ dnDirichlet( v(2.0, 2.0, 2.0, 2.0) )
Q := fnCodonGY94( kappa, omega, fnF3x4(pi1, pi2, pi3) )

See Also

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