1. A method for generating distances from aligned protein
sequences.
2. A method for calculating numbers of changes and including
them in parsimony trees.
3. Make general versions of drawgram and drawtree that simply
output vectors and labels, but do not attempt to make fonts. For
publication figures, I prefer to use Postscript directly, for better
control over linewidths, font sizes and types, etc. In addition, with
Postscript (or some general format), I can edit the position of the
labels so that they do not overlap. In this case, less is more. (It
would be very nice to have an option to output angles and lengths,
since they are easier to edit and preserve distances than pairs of x,y
coordinates.)
I have not had such serious problems with changing sequence
formats, because the text editor that I use (emacs) allows editing of
rectangles. I have had a lot of problems with trees however, and
some sort of a tree-editor, verifier, or some checking to make certain
that the tree includes as many species as the data, would be very
helpful.
Bill Pearson
