Mats.Sundvall at bmc.uu.se writes:
>Does somebody out there have some comments on how to compare evolutionary
>trees calculated by maximum parsimony algorithms. If I generate one
The best method I know for comparing phylogenetic trees
is Joseph Felsenstein's Maximum Likelihood method.
It has excellent statistical credentials.
It may not be practical if the data set is very large.
You also have to give it the n-way alignment as input.
J.F. distributes a package with several different tree methods on,
including max parsimony and max likelihood for DNA and protein:
Dept of Genetics, University of Washington, Seattle, Washington.
J. Felsenstein, Inferring Evolutionary Trees from DNA Sequences
in Statistical Analysis of DNA Sequnece Data
ed B.S.Weir, Marcel Dekker inc. p 133-150, 1983
L. Allison, Computer Science, Monash University, AUSTRALIA 3168