Some thoughts on what to do

[jhgillespie at ucdavis.edu]

In article <4413.9101251737 at crc.ac.uk> mbishop at crc.ac.uk (Martin Bishop)
writes:
>WHAT TO DO NEXT IN MOLECULAR PHYLOGENY RESEARCH
>
>Worry more about the processes by which molecular sequences change and
>less about getting the most parsimonious (but incorrect tree).

Here, here!! We have have known since '71 (Ohta and Kimura) that rates of
substitution vary.  We also know the the frequency of the four nucleotides vary
through time.  It is hard to imagine a characterization of the substitution
process that is farther from those assumed by most tree-construction
algorithms.

John Gillespie