[Biopython-dev] Calculating bootstrap values from a set of trees

Eric Talevich eric.talevich at gmail.com
Mon Sep 12 13:14:15 UTC 2011

Hi Peter,

On Mon, Sep 12, 2011 at 5:07 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> Hi Eric,
> I'm wondering if there is any code in Bio.Phylo for calculating
> bootstrap values from a set of trees?
> e.g. I have a master tree created from an alignment, and 1000
> bootstrap trees (created from 1000 re-sampled alignments). I want to
> annotate each branch with the number/percentage of times is it found
> in the 1000 bootsrap trees.

I haven't implemented this in Bio.Phylo yet, unfortunately. The closest
thing is Bio.Nexus.Trees.consensus. It would be worthwhile to port this to
Bio.Phylo eventually.

I once implemented this in python using binary strings to represent
> each branch as a split or partition of the nodes into two groups. I'm
> not sure where I put this script... but it pre-dated Bio.Phylo anyway.
> Alternatively, which standalone tool would you recommend for this?
I think Phylip's seqboot and consense will do the trick. Normally I let
RAxML do this sort of thing for me.


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