Rev Language Reference

• fnKimura80

fnK80(RealPos kappa)

kappa :	RealPos (pass by const reference)
	The transition/transversion rate.

RateMatrix

In this model, all nucleotides have an equal stationary frequency, and transition and transversion rates are allowed to be different. Its only parameter, kappa, codes for the ratio between the rate of transitions and transversions. The K80 rate matrix elements will be of the form: Q[i, j] = c * kappa, if i<->j is a transition = c, 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 ~ dnExp(0.5)

# create a K80 rate matrix
Q := fnK80(kappa)

• fnJC
• fnF81
• fnK81
• fnT92
• fnHKY
• fnGTR