Does anyone have the transition equations for Felsenstein's model of
sequence evolution implemented in Phylip 3.5c (F84), fastDNAml etc....
I have been playing with some but seem to be missing a scaling factor
involved in calculating beta?? (or possibly the branch lengths)
I hope someone can help...all my likelihoods are turning out wrong :-(
email: nicholas.grassly at pembroke.oxford.ac.uk