mortonjt/ete
ETE (Environment for Tree Exploration) is a python toolkit intended for tree analysis and visualization. It provides both a comprehensive API to manipulate and operate with trees in a programmatic way, as well as a number of command line tools to easily compare, annotate, modify or render tree images. ETE is currently developed as a research tool in the context of genomics and phylogenetics, providing several specific modules for orthology and paralogy prediction, NCBI taxonomy queries, multiple sequence alignment integration and more.