Pileup Dendogram Scale

Gabriel Romero ez008413 at dale.ucdavis.edu
Wed Nov 8 11:47:43 EST 1995

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.

Gabby Romero  

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