Rev Language Reference

fndNdS - Add a dN/dS factor to a codon rate matrix.

Constructs a rate matrix on the 61 non-stop codons (in the standard genetic code). Q(i,j) = Q'(i,j) * omega if aa(i) != aa(j) * 1 if aa(i) == aa(j) where aa(i) gives the amino acid for codon i in the standard genetic code, and Q'(i,j) is the input rate matrix on codons. The dNdS 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


fndNdS(RateMatrix submodel, RealPos omega)


submodel : RateMatrix (pass by const reference)
Singlet (i.e. nucleotide) rate matrix.
omega : RealPos (pass by const reference)
The dN / dS rate ratio.

Return Type


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 := fndNdS(fnX3(fnGTR(er, nuc_pi)), omega)         # GTR + X3 + dNdS

See Also