Mike Syvanen <syvanen at ucdavis.edu> writes:
>> Please correct an impression that I have carried around. I do not use ML
> methods, but after once hearing it described, I thought it worked on the same
> assumptions as did the traditional distance methods. Hence, there are just two
> categories of methods -- namely distance and parsimony. If this view is not
> correct, could someone provide a reference that describes ML (in grammatical
> sentences) and contrasts it to distance and parsimony methods.
ML is a character based method, which predicts the characters at each
node of the tree, just like parsimony. Unlike parsimony, it measures
the quality of the tree based on all the positions or characters, not
just the "informative" ones.
If you divide phylogenetic methods into distance-based and
character-based, ML is definately in the same character-based
group as parsimony.