Scott Knowles asks:
> From your experience, do you know whether software such as MacClade
> can handle DNA or AA sequence data? I would like to present some simple
> ideas about phylogeny, evolution, distance between species etc. to my
> freshman biology classes.
> Thanks in advance for your thoughts. Note that I'm a toxicologist with
> only slightly more experience in this area than my students :)
> Perhaps I need to read-up a bit more before I can even pose the right
The book (manual) which comes with MacClade is an excellent introduction
to the concepts of phylogenetic analysis using parsimony, although it
might be too much for freshpeople. I believe that "Part II. Phylogenetic
Theory" (pp. 25-129 of the 398 p. manual) is available as a separate
offprint. MacClade can certainly handle the mentioned types of molecular
data, and comes with sample data files, but the software is not intended
to be used for searches of minimum length trees. That is where PAUP
($100) and Phylip (free) come into use (to name two examples only).