[Biopython-dev] Rerooting a tree with Bio.Phylo

[Peter]

On Mon, Mar 22, 2010 at 8:28 PM, Eric Talevich <eric.talevich at gmail.com> wrote:
> On Mon, Mar 22, 2010 at 12:21 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:
>
>> Hi Eric,
>>
>> I've got a real example of a simple tree manipulation that I would like to
>> handle via your new module. I have a (small) unrooted tree from a gene
>> family in Newick format, which by construction includes an out-group
>> (the same gene but from a more distant organism). I would like to reroot
>> the tree so that this out-group is at the basal level.
>>
>> Can Bio.Phylo help me here?
>>
>
> In Bio.Nexus, would you normally have handled this with the method
> root_with_outgroup? I intend to port that method to Bio.Phylo once I
> understand it, but the existing code has been kind of hard for me to figure
> out.
>
> Let's address it here, then. Is there a detailed plain-text description
> somewhere of how this operation should work in general?

I've just got a quick answer for you now tonight: I've not used Bio.Nexus
to try and do this - I'll try to get back to you in more depth tomorrow.

Thanks,

Peter