Rev Language Reference

fnX2 - Construct a doublet (16x16) rate matrix from a nucleotide rate matrix.

Constructs a double rate matrix on the 16 nucleotide pairs. Rates of change from nucleotide i -> j at each doublet position are given by the nucleotide rate matrix. The rate of 2 simultaneous changes is 0. The X3 function can be used to constructor rate matrices on doublets in a modular fashion.


fnX2(RateMatrix submodel)


submodel : RateMatrix (pass by const reference)
Nucleotide rate matrix.

Return Type


kappa ~ dnLognormal(0,1)
nuc_pi ~ dnDirichlet( rep(2.0, 4) )
# Mutation rate matrix on RNA stems
Q1 := fnX2( fnHKY(kappa, nuc_pi) )
F ~ dnIID(16, dnNormal(0,1))
# Add selection to the rate matrix
Q2 := fnMutSel(Q1, F)

See Also