Rev Language Reference

• fnTamuraNei

fnTrN(RealPos kappa1, RealPos kappa2, Simplex baseFrequencies)

kappa1 :	RealPos (pass by const reference)
	The first transition rate (A<->G).
kappa2 :	RealPos (pass by const reference)
	The second transition rate (C<->T).
baseFrequencies :	Simplex (pass by const reference)
	The stationary frequencies of the states.
	Default : [ 0.250, 0.250, 0.250, 0.250 ]

RateMatrix

In this model, nucleotide base frequencies are different, and the two transition rates (A <-> G and C<->T) can be different to each other, and to the transversion rate. The first argument, kappa1, defines the ratio between the rate of A <-> G (i.e. purine) transitions to transversions. The second argument, kappa2, defines the ratio between the rate of C <-> T (i.e. pyrimidine) transitions to transversions. The third argument, baseFrequencies, defines the stationary frequencies of nucleotide bases. The TrN rate matrix elements are of the form: Q[i, j] = c * kappa1 * baseFrequencies[j], if i<->j is A<->G = c * kappa2 * baseFrequencies[j], if i<->j is C<->T = c * baseFrequencies[j], otherwise where c is a constant needed to normalize the average rate to 1

# A <-> G transition rate
kappaAG ~ dnLognormal(0,1)

# C <-> T transition rate
kappaCT ~ dnLognormal(0,1)

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

# create a TrN rate matrix
Q := fnTrN(kappaAG, kappaCT, ,pi)

• fnJC
• fnK80
• fnK81
• fnT92
• fnHKY
• fnGTR