Rev Language Reference

fnT92(RealPos kappa, Probability gc)

kappa :	RealPos (pass by const reference)
	The transition-tranversion rate ratio.
gc :	Probability (pass by const reference)
	The frequency of GC.

RateMatrix

In this model, A and T have an equal stationary frequency, with G and C frequencies distinct, 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, gc, codes for the compound frequency of G and C nucleotides. The T92 rate matrix elements will be of the form: Q[i, j] = c * kappa * gc / 2, if i<->j is a transition and j is C or G = c * gc / 2, if i<->j is a transversion and j is C or G = c * kappa * (1 - gc) / 2, if i<->j is a transition and j is A or T = c * (1 - gc) / 2, if i<->j is a transversion and j is A or T where c is a constant needed to normalize the average rate to 1.

# the ratio between rates of transitions and transversions
kappa ~ dnExp(0.5)

# the frequency of G and C nucleotides
gc ~ dnUnif(0, 1)

# create a T92 rate matrix
Q := fnT92(kappa, gc)

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• fnHKY
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• fnGTR