In article <nicholas.grassly-2010951613350001 at macws31.zps.ox.ac.uk>,
Nick Grassly <nicholas.grassly at pembroke.oxford.ac.uk> wrote:
>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've got the equations. They are in a manuscript of mine that is
in press at Molecular Biology and Evolution. You can ftp a copy of
the LaTeX source for that manuscript from directory pub/papers/hmc
in the ftp area of my workstation evolution.genetics.washington.edu.
The paper is hmc.tex. Even if you can't process LaTeX you could
read the source and figure it out.
For branch lengths I have always followed the practice (which everyone
seems to be converging on) of scaling them so that a tiny branch of
length x predicts a fraction x of difference betweent the DNA sequences
at the two ends of the branch.
Joe Felsenstein joe at genetics.washington.edu (IP No. 188.8.131.52)
Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA