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etetoolkit

Analyze and visualize phylogenetic trees using the ete3 library.

1|Updated Mar 11, 2026
Search Tags:#visualization#taxonomy#ete3#phylogenetics#tree-analysis#evolutionary-events
One-click install
npx skills add https://github.com/SciMate-AI/scicli --skill etetoolkit-scimate-ai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: etetoolkit
Source: https://github.com/SciMate-AI/scicli/tree/main/internal/skills/bundled/claude-scientific-skills/skills/etetoolkit
Command: npx skills add https://github.com/SciMate-AI/scicli --skill etetoolkit-scimate-ai

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires ete3, and includes scripts (resource) and references (resource) components.

What problem does it solve?

Phylogenetic data analysis often requires a consolidated workflow to manipulate trees, detect evolutionary events, annotate with taxonomy, and produce publication-ready visualizations. This skill provides a Python API and CLI utilities to streamline tree construction, analysis, and visualization using the ETE toolkit.

Core Features & Use Cases

  • Tree manipulation and analysis (load, prune, root, traverse, compute distances)
  • Evolutionary event detection (duplications/speciations) and orthology/paralogy workflows
  • NCBI Taxonomy integration for lineage annotation and topology construction
  • Comprehensive visualization support (PDF/SVG/PNG) with advanced layouts and faces
  • End-to-end workflows via Python APIs and CLI scripts for reproducible research

Quick Start

Load a gene tree with accompanying data, run basic topology operations, annotate leaves with taxonomy, and generate a publication-ready visualization.

Frequently Asked Questions about etetoolkit

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I visualize phylogenetic trees with taxonomy annotations in Python?▼

Visualize phylogenetic trees with taxonomy annotations using Python APIs and CLI scripts that load trees, integrate NCBITaxa lineages, and render publication-ready layouts to PDF, SVG, or PNG formats.

Can I detect evolutionary events like gene duplications and speciations in a phylogenetic tree?▼

Detect evolutionary events like duplications and speciations by applying tree manipulation and analysis operations that identify orthology and paralogy relationships within the phylogenetic topology.

Does ete3 support NCBITaxa integration for building taxonomic lineages?▼

Yes, ete3 supports NCBITaxa integration to annotate tree leaves with taxonomic lineages and construct topologies based on NCBI taxonomy databases for comparative genomics workflows.

What is the best way to root, prune, and traverse phylogenetic trees for comparative genomics?▼

Root, prune, and traverse phylogenetic trees for comparative genomics using streamlined command-line scripts and Python APIs that compute distances and perform topology operations end-to-end.

How do I generate publication-ready phylogenetic tree visualizations with advanced layouts?▼

Generate publication-ready phylogenetic visualizations with advanced layouts and faces by rendering annotated trees via the ete3 toolkit, supporting export to PDF, SVG, and PNG formats.

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