ETE3 * (Environment for Tree Exploration) is a major package and in particular Python package to navigate phylogenetic trees. It is the premier coding library/package for tree manipulation.
ETE4.0.0 beta has been released via GitHub. The download contains an old ETE manual (2009) and a README file for ETE4, thats about it. Does anyone know the location of the new ETE4 manual, or list of functionality beyond what is in the README (posted below). Reading the code is the last resort ;-)
- Read and write support for trees in Newick format
- Multiple functions for traversing, searching and manipulating tree topologies and node annotations
- Integration with NCBI Taxonomic database
- Integration with GTDB database
- Programmatic visualization framework
- Visualization of huge trees based on adaptive zooming
- Comparing trees
- Phylogenetic functions:
- orthology detection
- phylogenetic distance?
Reference * ETE 3: Reconstruction, analysis and visualization of phylogenomic data. Jaime Huerta-Cepas, Francois Serra and Peer Bork. Mol Biol Evol 2016; doi: 10.1093/molbev/msw046