What’s new in ETE 2.3

Update 2.3.2

New Modules


A collection of command line tools, implementing common tree operations has been added to the ETE core package. All tools are wrapped by the ete command, which should become available in your path after installation.

  • ete build: Build phylogenetic trees using a using a number of predefined built-in gene-tree and species-tree workflows. Watch example
  • ete view: visualize and generate tree images directly form the command line.
  • ete compare: compare tree topologies based on any node feature (i.e. name, species name, etc) using the Robinson-Foulds distance and edge compatibility scores.
  • ete ncbiquery: query the ncbi taxonomy tree directly from the database.
  • ete mod: modify tree topologies directly from the command line. Allows rooting, sorting leaves, pruning and more
  • ete annotate: add features to the tree nodes by combining newick and text files.
  • ete generate: generate random trees, mostly for teaching and testing

ncbi taxonomy

The new ncbi_taxonomy module provides the class NCBITaxa, which allows to query a locally parsed NCBI taxonomy database. It provides taxid-name translations, tree annotation tools and other handy functions. A brief tutorial and examples on how to use it is available here

New features

News in Tree instances

News in the treeview module

Highlighted Bug Fixes