DNA ML Questions

Xuhua Xia xxia1 at unix1.sncc.lsu.edu
Tue May 2 10:15:00 EST 1995

Joe Felsenstein (joe at evolution.genetics.washington.edu) wrote:

: >We've run trees on a various data sets of 37 taxa with over 2000
: >characters and found that the ML algorithm consistently gives us MUCH
: >lower bootstrap values...

: Possible explanations would be biases due to long-branch-attraction
: (the you-know-who Zone) in parsimony, or due to incorrect correction for
: multiple hits in distance methods.  Either might make there appear to
: be evidence for some groups in these methods that did not appear in
: ML (thought the latter might appear there too).

Why don't try the method in Ritland and Clegg (1990) to see if the data
are appropriate for resolving long branches? Does the observed "sequence
divergence" well reflect the "evolutionary divergence"?

Goldman and Yang (1994, and references therein) also offer methods for
quantifying rate heterogeneity, and their program implementing the discrete
gamma model is faster than one tends to think.

Xuhua Xia                         | 
Museum of Natural Science         | Phone: (504) 388-2841
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