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Re: advice for the undergrad
A few months ago I read a book review in Systematic Biology. That book was
about phylogenetic analysis using R. The idea is that while existing
programs are much more user-friendly, you might find that they can't answer
your very specific question, and in that case you're better off writing your
own program in R.
I'm not sure if anything is going to come out of this -- the review was not
unequivocally positive --, but still, "the worst math is no math at all",
and math with paleontological datasets sometimes requires programming.