[Biopython-dev] [Biopython - Feature #3218] (New) Bio.Phylo.Applications support for RAxML

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Issue #3218 has been reported by Eric Talevich.

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Feature #3218: Bio.Phylo.Applications support for RAxML
https://redmine.open-bio.org/issues/3218

Author: Eric Talevich
Status: New
Priority: Low
Assignee: Eric Talevich
Category: Main Distribution
Target version: Not Applicable
URL: 


RAxML is another popular tool for inferring phylogenies by maximum likelihood, and can be also be considered reasonably best-practice. Performance is good, and the command-line options are easy to understand. The Debian package for RAxML was uploaded to SVN today.

Let's create a wrapper for it in Biopython. The input is a Phylip alignment, like PhyML.

Homepage:
http://icwww.epfl.ch/~stamatak/index-Dateien/Page443.htm

NB: Frank Kauff wrote a separate wrapper for RAxML called PYRAXML. Check it out.
http://www.lutzonilab.net/downloads/

Implementation note: Phylip alignment format truncates taxon names, but we can support longer names in intermediate Bio.Align.MultipleSeqAlignment objects by mapping sequence IDs to unique integers (for example). That function would be useful in several places in Biopython.



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