Comparing distances for two trees

[areitzel]

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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[ppuigbo-2]

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.


(*) Puigbo P, Garcia-Vallve S, McInerney JO. Bioinformatics, 2007. 23:1556-1558.

2008/11/18 <areitzel@...>

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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http://www.bio.net/biomail/listinfo/mol-evol