Comparing topological congruence between RAxML and MrBayes trees

[Khaaliq DeJan]

Hi all,

I have trees created from RAxML and MrBayes and want to make
comparisons between the two. Does anyone know of software that
compares topological congruence between trees? Is anyone familiar with
tree-to-tree comparisons?

Any help is much appreciated!

Thanks,
Khaaliq DeJan

Research Assistant II
Santa Clara University
500 El Camino Real
Santa Clara, CA 95053

[Alexandros Stamatakis]

Hi Khaaliq,

Why don't you just compute the average Robinson Foulds distances between
the best-scoring ML tree and the posterior Bayesian trees?

RAxML has an option for doing this, but you may have to convert the
MrBayes output trees into a RAxML-readeble format which I guess, can be
done using Mesquite.

Another way of doing this would be to compute the RF distance between
the majority rule conesus trees, but RAxML can't do that because the
trees might potentially be multi-furcating, but I am sure that there
must be some software around that can do it.

Cheers,

Alexis

--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org

[Jenna Morgan Lang]

I've used treedist in Phylip for this sort of thing. See here:

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0062510

Jenna

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