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etetoolkit

Analyze phylogenetic trees with evolutionary event detection and NCBI taxonomy integration.

13|3|Updated Jun 10, 2026
Search Tags:#bioinformatics#evolutionary biology#phylogenetics#tree analysis#tree visualization
One-click install
npx skills add https://github.com/tassiovale/claude-code-kit --skill etetoolkit-tassiovale
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: etetoolkit
Source: https://github.com/tassiovale/claude-code-kit/tree/main/skills/etetoolkit
Command: npx skills add https://github.com/tassiovale/claude-code-kit --skill etetoolkit-tassiovale

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill simplifies complex phylogenetic tree analysis and visualization, enabling users to efficiently manipulate, analyze, and visualize phylogenetic trees.

Core Features & Use Cases

  • Tree Manipulation: Load, manipulate, and analyze hierarchical tree structures with support for Newick, NHX, PhyloXML, and NeXML formats.
  • Phylogenetic Analysis: Detect evolutionary events and perform orthology/paralogy analysis with integration of gene trees and multiple sequence alignments.
  • Taxonomy Integration: Access and integrate NCBI Taxonomy data for lineage retrieval and species tree construction.
  • Visualization: Create publication-quality tree visualizations in PNG, PDF, and SVG formats with custom styling and layout options.
  • Use Case: A researcher analyzing gene trees from a set of aligned sequences can use this Skill to automatically root the tree, identify evolutionary events, and visualize the results in a professional, customizable format.

Quick Start

Load your phylogenetic tree and alignment files, then execute the 'analyze' command within the etetoolkit skill.

Frequently Asked Questions about etetoolkit

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

FAQPage Schema
How do I analyze and visualize phylogenetic trees from Newick or NHX files?▼

To analyze and visualize phylogenetic trees, you can load Newick, NHX, PhyloXML, or NeXML files to manipulate hierarchical structures, detect evolutionary events, and render publication-quality visualizations in PNG, PDF, or SVG formats.

What is the best way to perform orthology and paralogy analysis on gene trees?▼

Orthology and paralogy analysis is performed by integrating gene trees with multiple sequence alignments to automatically detect evolutionary events and evaluate ortholog relationships within hierarchical phylogenetic structures.

Can I retrieve NCBI taxonomy lineage data and construct species trees?▼

Yes, NCBI taxonomy integration allows you to access and retrieve lineage data directly, enabling you to construct species trees and map taxonomic relationships onto your existing phylogenetic tree structures.

Does this phylogenetic tree analysis approach support multiple sequence alignment integration?▼

Yes, it supports multiple sequence alignment integration, allowing you to link aligned sequence data directly to gene trees for comprehensive evolutionary event detection and orthology analysis.

Do I need ete3 installed to manipulate and visualize phylogenetic trees?▼

Yes, ete3 is a required dependency for this toolkit, providing the necessary underlying framework to load, manipulate, and visualize phylogenetic trees and execute evolutionary analysis commands.

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