Rev Language Reference

fnGTR(Simplex exchangeRates, Simplex baseFrequencies)

exchangeRates :	Simplex (pass by const reference)
	The exchangeability rates between states.
baseFrequencies :	Simplex (pass by const reference)
	The stationary frequencies of the states.

RateMatrix

In this model, states are allowed to have different stationary frequencies, and exchangeability rates between states are allowed to be different. Its first argument, exchangeRates, codes for the transition rates between states (as in other models, transition rates are assumed to be symmetric). Its second argument, baseFrequencies, codes for the stationary frequencies of these states. Note that for n states, exchangeRates should have length n*(n-1)/2, and baseFrequencies should have length n. While this is usually used for DNA (and therefore has four states), the function can take any number of states, and therefore be used for many other applications (such as aminoacid or morphological evolution). The general time-reversible rate matrix elements will be of the form: Q[i, j] = c * exchangeRates[i, j] * baseFrequencies[j] where c is a constant needed to normalize the average rate to 1.

# exchange rates
er ~ dnDirichlet( v(1,1,1,1,1,1) )

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

# create a GTR rate matrix
Q := fnGTR(er,pi)

• fnJC
• fnK80
• fnK81
• fnT92
• fnHKY
• fnTrN