Last year, we published(*) a new software to compare phylogenetic trees that
may be useful for your project. The program is called TOPD/FMTS and it's
freely available at http://genomes.urv.cat/topd <http://genomes.urv.es/topd>
.
(*) Puigbo P, Garcia-Vallve S, McInerney JO. Bioinformatics, 2007.
23:1556-1558.
2008/11/18 <areitzel from whoi.edu>
> I am interested in comparing phylogenetic distances between two trees. The
> two
> trees are likelihood trees for different proteins, but each tree has the
> same
> taxa to facilitate pairwise comparisons. I was hoping someone could give
> me
> some advice on how to compare these two distance matrices. The trees do
> not
> have the same topology so the order of the taxa varies between the distance
> matrices for the two proteins. The goal for this project is to test for
> co-evolution of the two proteins via regression. Thanks in advance for any
> assistance.
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