[Biopython-dev] [Biopython - Feature #3216] (Closed) Bio.Phylo.Applications support for PhyML

[redmine at redmine.open-bio.org]

Issue #3216 has been updated by Eric Talevich.

Status changed from New to Closed
% Done changed from 0 to 100

Committed:
https://github.com/biopython/biopython/commit/b22304a40df4abfdf177af5e7d8fd4254d44833f

I also added a smidgen of documentation to the Tutorial.
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Feature #3216: Bio.Phylo.Applications support for PhyML
https://redmine.open-bio.org/issues/3216

Author: Eric Talevich
Status: Closed
Priority: Normal
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: Not Applicable
URL: http://www.atgc-montpellier.fr/phyml/


PhyML is another popular tool for inferring phylogenies by maximum likelihood, and can be also be considered reasonably best-practice (alongside RAxML, which isn't yet packaged). The Debian package for PhyML was recently updated to the latest version (3.0), and should be trickling down to the distros soon.

Let's create a wrapper for it in Biopython. The input is just a Phylip alignment, so this should be easier than MrBayes.


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