Building Consensus Trees Of Phyml Bootstraps

Question

[Marcus Shepheard]

Hey

I'm using PhyML to build phylogenetic trees of bacterial sequence data for me. However, when it generates bootstrap replicates it just dumps each replicate as a newick tree into a file. I'm wondering if anyone knows the easy way to transform these replicates into a single consensus tree?

Many thanks

Answer 1

[Paulo Nuin]

Use Consense, from the Phylip package to create a consensus tree. You can find more information here. Basically, what it does is to read all the trees and find the number of times each bnranch appeared and give you the percentage value.

[Michael Kuhn]

The added benefit is that you can easily parallelize this, while the PhyML MPI interface for bootstrapping didn't work for me.

[Marcus Shepheard]

Thank you for your answers, I'll have a play with this.

Answer 2

[Dejian]

The latest version (phyml-20110919.tar.gz) of PhyML can generate a consensus tree after bootstrapping. I am new to PhyML and I did not try earlier versions.

Answer 3

[2184687-1231-83-]

You can also try treebest mmerge, on sourceforge

[Marcus Shepheard]

I tried to find this but got not hits, do you have a link I could use? Thanks.

[2184687-1231-83-]

http://treesoft.sourceforge.net/treebest.shtml#install

[Adrian Pelin]

It's not obvious to me from the DOCs how to use this mmerge function. As for Consense from PHYLIP package, it seems to give higher percentage values than Geneious Tree Builder. I wish I could find one more algorithm to calculate the consensus tree.

Answer 4

[aidan-budd]

You can also do this using clann

http://bioinf.nuim.ie/clann/