Mrbayes: Consensus Trees Comparison

Question

[Alice]

Hello, biostars! Imagine, if you have several consensus trees from several MCMC runs implemented in MrBayes (4 for example). All analyses were different, under different models and priors. Now you want to compare topology of your trees. They are very long and it's difficult task for eyes to compare such ramous, long trees. First of all (as usually I do) - googling. I found package for Mesquite, but It's "under construction" science 2001 and not included in available mesquite version.

What would you do? Any packages, scripts or something?

Answer 1

[Andrzej Zielezinski]

I highly recommend Dendroscope. It calculates a final consensus tree from a set of large trees (e.g. consensus trees calculated from MrBayes). The program can be used interactively or in command-line mode.

If you are in a hurry use METATREE for comparing multiple alternative phylogenies.

[Alice]

Thank you very much! I simply forgot about dendroscope.

[Cacau]

Yes, Dendroscope is a very nice software which allows you to visualize a a tree with a large number of nodes. FigTree is also a nice choice.

Answer 2

[Alice]

Answering myself.

So, as usual, for such an aim there are some functions in R:

• compare.phylo (in the package phyloch)
• phylo.diff (in distory)