reflect-phylo-hmm.R
In rphast: Interface to 'PHAST' Software for Comparative Genomics

#state.names <- c("neutral", "conserved", "codon1", "codon2", "codon3")
#h <- hmm(t(matrix(c(0.95, 0.04, 0.01, 0, 0, 
#                    0.04, 0.95, 0.01, 0, 0,
#                    0,    0,    0,    1, 0,
#                    0,    0,    0,    0, 1,
#                    0.005, 0.005,  0.99,   0, 0), nrow=5,
#                  dimnames=list(state.names, state.names))))
#         eq.freq=c(0.6, 0.3, 0.1/3, 0.1/3, 0.1/3))
#reflect.phylo.hmm(h, c("neutral", "conserved"))