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

[Peter Cock]

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 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?

Thanks,

Peter