Editing Biopython (section)

=== Phylogeny ===

[[File:Phylo.draw.png|thumb|300px|Figure 1: A rooted phylogenetic tree created by Bio.Phylo showing the relationship between different organisms' Apaf-1 homologs<ref name="Zmasek2007">{{cite journal |last1=Zmasek |first1=Christian M |last2=Zhang |first2=Qing |last3=Ye |first3=Yuzhen |last4=Godzik |first4=Adam |date=24 October 2007 |title=Surprising complexity of the ancestral apoptosis network |journal=Genome Biology |volume=8 |issue=10 |doi=10.1186/gb-2007-8-10-r226 |pages=R226 |pmid=17958905 |pmc=2246300 |doi-access=free }}</ref>]]

[[File:Phylo.draw graphviz.png|thumb|Figure 2: The same tree as above, drawn unrooted using Graphviz via Bio.Phylo]]

The Bio.Phylo module provides tools for working with and visualising [[phylogenetic tree]]s.  A variety of file formats are supported for reading and writing, including [[Newick format|Newick]], [[Nexus file|NEXUS]] and [[phyloXML]].  Common tree manipulations and traversals are supported via the <code>Tree</code> and <code>Clade</code> objects.  Examples include converting and collating tree files, extracting subsets from a tree, changing a tree's root, and analysing branch features such as length or score.<ref name="Talevich2012">{{cite journal |last1=Talevich |first1=Eric |last2=Invergo |first2=Brandon M |last3=Cock |first3=Peter JA |last4=Chapman |first4=Brad A |date=21 August 2012 |title=Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython |url= |journal=BMC Bioinformatics |volume=13 |issue=209 |pages=209 |doi=10.1186/1471-2105-13-209 |pmid=22909249 |pmc=3468381 |doi-access=free }}</ref>

Rooted trees can be drawn in [[ASCII art|ASCII]] or using [[matplotlib]] (see Figure 1), and the [[Graphviz]] library can be used to create unrooted layouts (see Figure 2).