etetoolkit

Analyze and manipulate phylogenetic trees using Python's ete3 library.

22|4|Updated May 25, 2026

Search Tags:#visualization #taxonomy #ete3 #phylogenetics #tree-analysis #evolutionary-events

Ready to run

npx skills add https://github.com/crazymsn/academic-skills --skill etetoolkit-crazymsn

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: etetoolkit
Source: https://github.com/crazymsn/academic-skills/tree/main/academic-skills/etetoolkit
Command: npx skills add https://github.com/crazymsn/academic-skills --skill etetoolkit-crazymsn

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Phylogenetic analysis often requires manual handling of tree topology, annotations, and visualizations across multiple tools; ETE Toolkit consolidates these tasks into a single Python toolkit for end-to-end phylogenetic workflows.

Core Features & Use Cases

Tree IO, traversal, manipulation, and evolutionary-event detection for gene and species trees.
Taxonomy integration with NCBITaxa, alignment linking, and topology building for comprehensive phylogenomic pipelines.
Advanced visualization and reporting with rectangular and circular layouts, faces, legends, and publication-ready figures.

Quick Start

Load a tree using PhyloTree and render a basic figure to PDF.

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 in Python for publication?▼

ETE toolkit renders phylogenetic trees into publication-ready figures using rectangular and circular layouts, faces, and legends. It handles tree IO, manipulation, and visualization for gene and species trees in a single Python workflow.

What is the best way to detect evolutionary events on a phylogenetic tree?▼

Detecting evolutionary events on a phylogenetic tree is handled through ETE classes like PhyloTree and ClusterTree, which enable tree traversal and evolutionary event detection across gene and species trees.

Can I integrate NCBI taxonomy data with my phylogenetic tree analysis?▼

You can integrate NCBI taxonomy data with phylogenetic tree analysis using the NCBITaxa class, enabling taxonomy integration, alignment linking, and topology building for comprehensive phylogenomic pipelines.

Do I need Python and ete3 installed to analyze tree topology and manipulate branches?▼

Yes, you need Python and the ete3 library installed to analyze tree topology and manipulate branches. The Skill uses ETE classes like Tree and PhyloTree for traversal and manipulation.

Why use a Python toolkit for phylogenetic analysis instead of separate tree manipulation tools?▼

Using a Python toolkit for phylogenetic analysis consolidates manual handling of tree topology, annotations, and visualization across multiple tools into a single end-to-end workflow for evolutionary insights.