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

redmine at redmine.open-bio.org redmine at redmine.open-bio.org
Sun Jun 19 03:47:24 UTC 2011

Issue #3216 has been updated by Eric Talevich.

File _Phyml.py added
Assignee changed from Eric Talevich to Biopython Dev Mailing List
Priority changed from Low to Normal

I took a crack at this today. To test it, put this file into Bio/Phylo/Applications, add a blank __init__.py, and run it like this:

>>> from Bio import Phylo
>>> from Bio.Phylo.Applications._Phyml import PhymlCommandline
>>> cmd = PhymlCommandline(input='Tests/Phylip/random.phy')
>>> cmd()
>>> tree = Phylo.read('Tests/Phylip/random.phy', 'newick')
>>> Phylo.draw_ascii(tree)

It prints a lot of junk to stdout. The output tree takes the name <input>_phyml_tree.txt, and I don't see the option for changing the output file name.

There are some more comments sprinkled through the source, and I'm still not sure how to handle the '-f' option.

Feature #3216: Bio.Phylo.Applications support for PhyML

Author: Eric Talevich
Status: New
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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