[Biopython-dev] Bio.Cluster.Tree -> Bio.Phylo

Eric Talevich eric.talevich at gmail.com
Mon Apr 16 22:15:14 UTC 2012

On Mon, Apr 16, 2012 at 12:48 PM, Andrew Sczesnak
<andrew.sczesnak at med.nyu.edu> wrote:
> Hi Eric,
> I was playing with Bio.Cluster recently and noticed that trees generated by
> that module are not compatible with Bio.Phylo. I think it would be useful if
> output from Cluster could be manipulated with Phylo.
> At first glance, it doesn't seem like it would be that tricky to add a
> method of converting Bio.Cluster tree objects to Bio.Phylo tree objects, and
> I would be happy to work on this. Before making an attempt, I wanted to get
> your feedback on whether you think this would be useful and if you had
> anything similar in the works already.
> Best,
> Andrew

Hi Andrew,

Interesting idea. It would be simple enough to add a "from_cluster"
function or class method to either Phylo/BaseTree.py or
Phylo/_utils.py. But as every scientist knows, just because we can
doesn't necessarily mean we should. Do you have a specific use case in

If the main idea is to use Bio.Cluster to generate trees based on a
measure of sequence distance, we could probably do more to support
that. This code might also be worth posting on wiki "Phylo cookbook"
page (http://www.biopython.org/wiki/Phylo_cookbook) to get more eyes
on it while we consider merging it into the main distribution.


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