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 inferring phylogenetic trees
is Joseph Felsenstein's Maximum Likelihood method.
It has excellent statistical credentials.
You have to give it the n-way alignment as input.
It may not be practical if the data set is very large.
On the other hand if you want to choose between a few given
trees it would be much faster.
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 Sequence Data
ed B.S.Weir, Marcel Dekker inc. p 133-150, 1983
L. Allison, Computer Science, Monash University, AUSTRALIA 3168