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ETE Toolkit 4 Phylogenetic Tree Analysis

Guides Claude to analyze, edit, compare, annotate, and visualize existing phylogenetic trees with ETE 4.4.0.

Data & AnalyticsAdvanced★ 33,030⑂ 3,248AI score 8/10Last updated: Aug 9, 2026

What it does

  • Reads/writes Newick and Nexus trees with the correct parser, annotates nodes via add_prop(), prunes, and reroots (e.g. midpoint outgroup).
  • Compares topologies with Robinson-Foulds, reporting normalized RF and shared leaf sets.
  • Detects duplication/speciation events in gene trees with PhyloTree and supports species-tree reconciliation.
  • Queries local NCBI and GTDB taxonomy databases for name→taxid translation and taxonomic topologies.
  • Visualizes via interactive SmartView, static PNG screenshots, or Qt-rendered PDF/SVG vectors.
  • Includes an ETE3→ETE4 migration reference so old idioms (ete3, format=, tree & "name") aren't reused.

Who it's for

  • Phylogenetics and comparative genomics researchers or graduate students.
  • Anyone post-processing IQ-TREE/FastTree output into publication figures.
  • Developers porting legacy ETE3 scripts to ETE4.

Examples

  1. "Load tree.nw keeping internal node names, prune to these 20 taxa while preserving branch lengths" → generates prune(preserve_branch_length=True) code plus validation checks.
  2. "Compute the RF distance between these two inferred trees and report the normalized value" → uses robinson_foulds() after checking for duplicate/empty leaf names.
  3. "List gene duplication events, then export a circular PNG colored by support values" → get_descendant_evol_events() plus scripts/quick_visualize.py --mode circular.

Note: it does not align sequences or infer trees — build the tree first with MAFFT/IQ-TREE.

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/etetoolkit/SKILL.md

What I want: (describe your task here)

If Claude can't open the link, open it yourself and paste the contents instead.

↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on AI Skill Mart.
Copy the skills/etetoolkit folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/etetoolkit/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git && mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/etetoolkit ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Open a terminal and create the skills folder: mkdir -p ~/.claude/skills
  2. Clone the repository: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  3. Copy just this skill: cp -r scientific-agent-skills/skills/etetoolkit ~/.claude/skills/
  4. Verify Python 3.10 or newer: python3 --version
  5. Install ETE 4: uv pip install "ete4==4.4.0" (add ete4[render-sm] for PNG screenshots, ete4[treeview] for PDF/SVG).
  6. Check the install: uv run --with "ete4==4.4.0" python -c "import ete4; print(ete4.__version__)"
  7. Restart Claude Code, then ask something like "prune this Newick tree with ETE4" to trigger the skill.
  8. NCBI/GTDB taxonomy features download large public datasets on first use — ensure network access and free disk space.
View source on GitHub ↗License: MIT