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etetoolkit

Automate phylogenetic tree analysis and visualization with the ETE toolkit.

Updated Dec 17, 2025
Search Tags:#bioinformatics#phylogenetics#tree analysis#evolutionary analysis#tree visualization
One-click install
npx skills add https://github.com/robotlearning123/claude-scientific-skills --skill etetoolkit-robotlearning123
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: etetoolkit
Source: https://github.com/robotlearning123/claude-scientific-skills/tree/main/scientific-skills/etetoolkit
Command: npx skills add https://github.com/robotlearning123/claude-scientific-skills --skill etetoolkit-robotlearning123

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires ete3, pypdf, pdfplumber, pdf2image, and includes scripts (resource) and references (resource) components.

What problem does it solve?

The etetoolkit Skill streamlines the process of analyzing and visualizing phylogenetic trees, making complex tasks like tree manipulation, evolutionary event detection, and taxonomy integration more accessible.

Core Features & Use Cases

  • Tree Manipulation: Load, manipulate, and analyze hierarchical tree structures.
  • Phylogenetic Analysis: Detect duplication and speciation events, identify orthologs and paralogs.
  • NCBI Taxonomy Integration: Access and integrate taxonomic information from the NCBI Taxonomy database.
  • Tree Visualization: Create publication-quality tree visualizations in PNG, PDF, and SVG formats.
  • Use Case: Suppose you have a gene tree and want to detect speciation events and annotate it with NCBI taxonomy information. This Skill can perform these tasks efficiently.

Quick Start

Run the script 'tree_operations.py' with the command: python scripts/tree_operations.py reroot input_tree.nw output_tree.nw --midpoint

Frequently Asked Questions about etetoolkit

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

FAQPage Schema
How do I reroot a phylogenetic tree using a Newick file?▼

Reroot a phylogenetic tree by running the tree_operations.py script with the reroot command, passing the input tree.nw file, output path, and the --midpoint flag to generate a rerooted Newick tree.

Can I detect duplication and speciation events in a gene tree automatically?▼

Yes, phylogenetic analysis can detect duplication and speciation events, identify orthologs and paralogs, and annotate trees with NCBI taxonomy information by applying ETE toolkit functions to gene tree structures.

What is the best way to visualize phylogenetic trees for publication?▼

Visualize phylogenetic trees for publication by creating high-quality outputs in PNG, PDF, and SVG formats, utilizing the ETE toolkit's tree visualization capabilities integrated with pdfplumber and pdf2image dependencies.

Does ete3 work with NCBI taxonomy database integration for tree annotation?▼

Yes, ete3 supports NCBI Taxonomy integration, allowing users to access and integrate taxonomic information directly from the NCBI Taxonomy database to annotate hierarchical tree structures.

What Python dependencies do I need to install for evolutionary tree analysis?▼

Evolutionary tree analysis requires installing ete3 for tree manipulation, along with pypdf, pdfplumber, and pdf2image for processing and generating PDF visualization outputs from the phylogenetic data.

How do I load and manipulate hierarchical tree structures in Python?▼

Load and manipulate hierarchical tree structures in Python by utilizing the ETE toolkit's tree manipulation functions, which support loading Newick files, performing rerooting operations, and applying taxonomic annotations.

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