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 approach I know of as yet is the maximum likelihood method
of Joseph Felsenstein Dept of Genetics, Uni of Washington, Seattle
eg "Inferring Evolutionary Trees from DNA Structures"
Statistical Analysis of DNA Sequence Data
(ed) B. S. Weir, Marcel Dekker inc 1983 p133-150
This has excellent statistical validity.
It may not be practical if your tree is very big.
JF distributes a package containing several tree building methods
for free. This includes a parsimony method and a M.L. method.
Lloyd Allison, Computer Science, Monash University, AUSTRALIA 3168