How can I put a scale on the dendogram generated by pileup? I have used
distances to compute the pairwise rates of substitutions. I aligned
protein sequences and the figures I got are around 80 substitutions per
100 amino acids. Does this rate mean # base substitutions per 300 bases
(=100 amino acids)? To quantify homology on the dendogram, should I just
manually write the rates of substitutions at the branch points of the
tree (using averages for inter-cluster comparison)? Alternatively, what
is the most convenient way to simply put a scale underneath the dendogram?
Thanks for any help.