Rev Language Reference

fnHKY(RealPos kappa, Simplex baseFrequencies)

kappa :	RealPos (pass by const reference)
	The transition-transversion rate ratio.
baseFrequencies :	Simplex (pass by const reference)
	The stationary frequencies.

RateMatrix

In this model, nucleotides have different stationary frequencies, and transition and transversion rates are allowed to be different. Its first parameter, kappa, codes for the ratio between the rate of transitions and transversions. Its second parameter, baseFrequencies, codes for the frequencies of each nucleotide. The HKY rate matrix elements will be of the form: Q[i, j] = c * kappa * baseFrequencies[j], if i<->j is a transition = c * baseFrequencies[j], if i<->j is a transversion where c is a constant needed to normalize the average rate to 1.

# the ratio between rates of transitions and transversions
kappa ~ dnLognormal(0,1)

# the base frequencies
pi ~ dnDirichlet( v(1,1,1,1) )

# create an HKY rate matrix
Q := fnHKY(kappa,pi)

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