etetoolkit

SUMMARY

What it does

This Agent Skill provides procedural guidance for using the ETE 4 toolkit to analyze, manipulate, compare, annotate, and visualize phylogenetic or other hierarchical trees. The skill's source documentation (SKILL.md) describes capabilities including Newick/Nexus tree I/O, topology editing and pattern matching, Robinson-Foulds comparisons, gene-tree evolutionary events and reconciliation, NCBI/GTDB taxonomy queries, SmartView exploration, and publication rendering. It explicitly states that ETE does not replace sequence alignment or phylogenetic inference software, and that raw sequences should first be aligned and a tree inferred using other tools. The skill targets ETE 4.4.0 and includes bundled scripts for tree operations and visualization. The source is licensed under GPL-3.0-or-later and is part of the K-Dense-AI scientific-agent-skills repository.