Tuesday, October 5, 2010

Bio.Phylo: A unified phylogenetics toolkit for Biopython

I presented this at the Bioinformatics Open Source Conference (BOSC 2010) in early July, but somehow forgot to post it here too. It's an overview of my somewhat new sub-package for working with phylogenetic trees in Biopython, based on my Google Summer of Code 2009 project (a phyloXML parser in Biopython).

In a nutshell, Bio.Phylo is a library for manipulating finished phylogenetic trees and integrating them into a Biopython-based workflow. It can handle the standard file formats — Newick, Nexus and phyloXML, with the current exception of NeXML — and has particularly good support for phyloXML.

This presentation walks through an example of loading a Newick tree, viewing it a few different ways, adding branch colors, and saving it as a phyloXML file.

The conference abstract is here. I also recommend the main documentation in the Biopython Tutorial (see chapter 12) and the wiki page.