Path: utzoo!attcan!uunet!munnari.oz.au!bruce!lloyd
From: lloyd@bruce.OZ (lloyd allison)
Newsgroups: bionet.molbio.evolution
Subject: Re: How to compare trees
Message-ID: <1952@bruce.OZ>
Date: 19 Mar 90 01:07:14 GMT
References: <3067.2602a4ec@bmc.uu.se>
Organization: Monash Uni. Computer Science, Australia
Lines: 25

Mats.Sundvall@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.

see
   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

zzz