posterior probability of a MCC tree

[Ed]

Hi all,

Is there any way to get the posterior probability of a phylogeny (not clade)? I'd like to come up with a number that summarizes the overall support in a phylogeny given a distribution of trees.

Thanks,

Eduardo

[Andrew Rambaut]

Hi Eduardo,

There is a program in the BEAST package called 'treeloganalyser' (it is command-line only and can be found in the bin/ directory). You can run it on your set of trees and it will give you the probability of each unique topology in descending order.

This will only work on relatively small data sets or larger data sets with extremely strong signal otherwise you will tend to find that every tree in the sample is unique.

Andrew

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[Eduardo Castro Nallar]

Thanks for the reply Andrew. Is it possible to specify a target tree? I guess if my target tree, in this case the MCC, is present in the distribution then I can get its posterior probability.

Eduardo

[Alexei Drummond]

Dear Eduardo,

There is a quite accurate method to compute the probability of individual trees based on "conditional clade probabilities" that can work even when the trees are large.

Check out the following two papers:

Hohna S, Drummond AJ (2012) Guided tree topology proposals for Bayesian phylogenetic inference, Systematic Biology 61:1

Larget B. (2013) The estimation of tree posterior probabilities using conditional clade probability distributions. Systematic biology, 62:501-511.

I am planning on implementing this method in a new version of TreeLogAnalyzer in the next couple of months. Maybe somebody on the user group already knows of existing implementations that are easy to use?

Cheers
Alexei

[Eduardo Castro Nallar]

Dear Alexei,

Thanks for the reply. I'll check this papers out. Bret's method is already implemented in a software written by himself called ccdprobs available here

Cheers,

Eduardo