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ETE Toolkit 4 Phylogenetic Trees

Guides Claude to read, edit, compare, annotate, and visualize phylogenetic trees with ETE 4.

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

What it does

  • Newick/Nexus I/O with deliberate parser= choice so internal names, support values, and branch lengths survive round-trips
  • Traversal, node annotation via add_props, midpoint/outgroup rooting, and pruning with optional branch-length preservation
  • Robinson-Foulds topology comparison and repeated-subtree search with TreePattern
  • Gene-tree duplication/speciation event detection via PhyloTree plus species-tree reconciliation
  • NCBI and GTDB taxonomy queries and taxonomic topology building
  • Interactive SmartView exploration, PNG screenshots, and Qt-based vector PDF/SVG rendering
  • Bundled CLI scripts (tree_operations.py, quick_visualize.py) for one-line stats, convert, reroot, prune, compare, and plot

Who it's for

  • Phylogenetics, evolutionary biology, and microbial genomics researchers
  • Anyone producing reproducible, publication-ready tree figures
  • Developers porting legacy ETE 3 scripts to the ETE 4 API

Examples

  1. "Prune tree.nw to my 30 focal taxa while preserving branch lengths, midpoint-root it, and write the result."
  2. "Compare the ML and Bayesian trees with Robinson-Foulds and report the normalized RF plus shared leaf set."
  3. "Parse species as the prefix before | in this gene tree, list duplication/speciation events, and render a circular SmartView PNG with support coloring."

· · · Install guide · · ·

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 Claude 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 go to your home directory: cd ~
  2. Clone the repository: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  3. Create the skills folder: mkdir -p ~/.claude/skills
  4. Copy just this skill: cp -r scientific-agent-skills/skills/etetoolkit ~/.claude/skills/
  5. Make sure you have Python 3.10+, then install the library: uv pip install "ete4==4.4.0" (add ete4[render-sm] for PNG, ete4[treeview] for PDF/SVG)
  6. Verify: uv run --with "ete4==4.4.0" python -c "import ete4; print(ete4.__version__)"
  7. Restart Claude Code and ask something like "analyze this Newick tree with ETE4" to trigger the skill.
  8. For NCBI/GTDB taxonomy, allow network access and several GB of disk space on first database update.
View source on GitHub ↗License: MIT