ETE Cookbook

This document provides real-case examples, tips and tricks on how to use the ete-tools and the ETE Python API.
This is a work continuously in progress. If you feel like contributing with fixes or new recipes, please get in touch and join us at this cookbook repository.
Using manual alignments
Building species trees (Concatenated alignments)
Available workflows and apps
List workflows, apps and configurations
Tips, troubleshooting and debuging:
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