[Biopython] Bio.Phylo: midpoint root?
Tanya Golubchik
golubchi at stats.ox.ac.uk
Thu May 31 12:10:21 UTC 2012
Thanks, Eric - will have a go!
T
On 31/05/12 05:36, Eric Talevich wrote:
> On Wed, May 30, 2012 at 10:55 AM, Eric Talevich <eric.talevich at gmail.com
> <mailto:eric.talevich at gmail.com>> wrote:
>
> On Wed, May 30, 2012 at 9:40 AM, Tanya Golubchik
> <golubchi at stats.ox.ac.uk <mailto: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
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