Phylogenetics in Biopython: Filling in the gaps

by Yanbo Ye for National Evolutionary Synthesis Center (NESCent)

Biopython is a set of open source python packages and modules for bioinformatics works. In the Bio.Phylo package, there are already implementations for some basic phylogenetics tasks: basic tree operations, parsers for Newick, Nexus and PhyloXML, and wrappers for Phyml, Raxml and PAML. While there are some important components that remain to be implemented to better support phylogenetic workflows. These include simple tree construction algorithms, consensus tree searching, and tree visualization.