Rev Language Reference

Constructs a rate matrix on the 61 non-stop codons (in the standard genetic code). Rates of change from nucleotide i -> j at each codon position are given by the nucleotide rate matrix. The rate of 2 or 3 simultaneous changes is 0. The X3 function can be used to construct other rate matrices in a modular fashion. For example: (i) MG94 = F81 + X3 + dNdS (ii) MG94K = HKY85 + X3 + dNdS

kappa ~ dnLognormal(0,1)
omega ~ dnUniform(0,1)
nuc_pi ~ dnDirichlet( rep(2.0, 4) )
Q1 := fnCodonMG94K( kappa, omega, nuc_pi )
# This is the same.
Q2 := fndNdS(fnX3(fnHKY(kappa, nuc_pi)), omega)          # HKY + X3 + dNdS, or HKY*3 + dNdS

er ~ dnDirichlet( v(1,1,1,1,1,1) )
Q3 := fnX3(fnGTR(er, nuc_pi))      # GTR + X3, or GTR*3