Question: Building Consensus Trees Of Phyml Bootstraps
5
gravatar for Marcus Shepheard
9.6 years ago by
Imperial College London
Marcus Shepheard50 wrote:

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

consensus phylogenetics • 6.7k views
ADD COMMENTlink modified 7.2 years ago by aidan-budd1.9k • written 9.6 years ago by Marcus Shepheard50
5
gravatar for Paulo Nuin
9.6 years ago by
Paulo Nuin3.7k
Canada
Paulo Nuin3.7k wrote:

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.

ADD COMMENTlink written 9.6 years ago by Paulo Nuin3.7k

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

ADD REPLYlink written 9.6 years ago by Michael Kuhn5.0k

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

ADD REPLYlink written 9.6 years ago by Marcus Shepheard50
2
gravatar for Dejian
8.4 years ago by
Dejian1.3k
United States
Dejian1.3k wrote:

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.

ADD COMMENTlink written 8.4 years ago by Dejian1.3k
1
gravatar for 2184687-1231-83-
9.6 years ago by
2184687-1231-83-5.0k wrote:

You can also try treebest mmerge, on sourceforge

ADD COMMENTlink written 9.6 years ago by 2184687-1231-83-5.0k

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

ADD REPLYlink written 9.6 years ago by Marcus Shepheard50

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

ADD REPLYlink modified 7 months ago by RamRS26k • written 9.6 years ago by 2184687-1231-83-5.0k

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.

ADD REPLYlink written 5.2 years ago by Adrian Pelin2.4k
1
gravatar for aidan-budd
7.2 years ago by
aidan-budd1.9k
Germany
aidan-budd1.9k wrote:

You can also do this using clann

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

ADD COMMENTlink written 7.2 years ago by aidan-budd1.9k
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