etetoolkit
Analyze, manipulate, compare, annotate, and visualize phylogenetic or other hierarchical trees with ETE 4. Use for Newick/Nexus tree I/O, topology edits and pattern matching, Robinson-Foulds comparisons, gene-tree evolutionary events and reconciliation, NCBI/GTDB taxonomy, SmartView exploration, and publication rendering. Do not use it to infer trees from raw sequences; align sequences and infer a tree first.
- Version
- 2.1
- License
- GPL-3.0-or-later
- Compatibility
- Bundled scripts require Python 3.10+ and ete4 4.4.0 (upstream ete4 supports Python >=3.7). Taxonomy setup and SmartView exploration need network access; static SmartView PNG rendering needs ete4[render-sm], and Qt PDF/SVG rendering needs ete4[treeview].
Pinned to revision 70a605012eee, so it is the text this page describes rather than whatever the author pushed since.
Pre-approved tools experimental
Experimental field. Support varies between clients, so this list is what the author declared, not what your client will enforce.
- Read
- Write
- Edit
- Bash
- Python
Files
- skills/etetoolkit/SKILL.md
- skills/etetoolkit/references/api_reference.md
- skills/etetoolkit/references/migration-ete3-to-ete4.md
- skills/etetoolkit/references/taxonomy.md
- skills/etetoolkit/references/visualization.md
- skills/etetoolkit/references/workflows.md
- skills/etetoolkit/scripts/quick_visualize.py
- skills/etetoolkit/scripts/tree_operations.py
Every link opens the file at its source, pinned to the revision this page describes.