[Biopython] Bio.Phylo: midpoint root?

[Eric Talevich]

On Wed, May 30, 2012 at 10:55 AM, Eric Talevich <eric.talevich at gmail.com>wrote:

> On Wed, May 30, 2012 at 9:40 AM, Tanya Golubchik <golubchi at stats.ox.ac.uk>wrote:
>
>> Hello,
>>
>> Does anyone have a quickie method for calculating the midpoint root of a
>> given tree?
>>
>>
> It's been on my to-do list. (The first step was adding the keyword
> argument 'outgroup_branch_length' to root_with_outgroup.) The tree method
> 'depths' should also be handy.
>
> The algorithm I had in mind looks like:
>
<madness>

>
> I too would be delighted to see a better algorithm for this.
>
>
I implemented this in an intuitive but very inefficient way, calculating
the pairwise distances between all tips of the tree. You can try it from
git:
https://github.com/biopython/biopython/commit/94c128bd428cc5d53b50edd1d2e4730ee212f530

It would still be nice to see a better algorithm, if anyone has one on hand.

-E