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etetoolkit

Manipulate, analyze, and visualize phylogenetic trees using Python.

8|Updated Nov 19, 2025
Search Tags:#bioinformatics#visualization#evolutionary biology#phylogenetics#ete toolkit#tree analysis
One-click install
npx skills add https://github.com/sanand0/scientific-research --skill etetoolkit-sanand0
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: etetoolkit
Source: https://github.com/sanand0/scientific-research/tree/main/.claude/skills/etetoolkit
Command: npx skills add https://github.com/sanand0/scientific-research --skill etetoolkit-sanand0

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill simplifies complex phylogenetic tree manipulation, analysis, and visualization, making advanced phylogenomics accessible.

Core Features & Use Cases

  • Tree Manipulation: Load, modify, and save trees in various formats (Newick, NHX, etc.).
  • Phylogenetic Analysis: Detect evolutionary events (duplication, speciation), identify orthologs.
  • Taxonomy Integration: Connect trees with NCBI taxonomy for annotation.
  • Visualization: Generate publication-quality tree figures (PDF, SVG, PNG).
  • Use Case: Analyze gene family evolution by detecting duplications, identifying orthologs across species, and visualizing the resulting phylogenetic tree with annotated evolutionary events.

Quick Start

Use the etetoolkit skill to visualize the tree in 'my_tree.nw' as a PDF file.

Frequently Asked Questions about etetoolkit

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

FAQPage Schema
How do I visualize a phylogenetic tree and export it as a PDF?▼

To visualize a phylogenetic tree, load your Newick or NHX file and use the Python toolkit to render publication-quality figures directly to PDF, SVG, or PNG files.

How do I detect evolutionary events like gene duplication and speciation in a phylogenetic tree?▼

Detect evolutionary events like gene duplication and speciation by analyzing your phylogenetic tree with Python scripts that automatically identify these events and locate orthologs across species.

Can I integrate NCBI taxonomy data to annotate my phylogenetic tree?▼

Yes, you can integrate NCBI taxonomy data to annotate your phylogenetic tree. The toolkit connects your tree structures directly with the NCBI taxonomy database for comprehensive species annotation.

What is the best way to manipulate and save phylogenetic trees in Newick format using Python?▼

The best way to manipulate phylogenetic trees is using a Python toolkit that supports loading, modifying, and saving tree structures across various standard formats like Newick and NHX.

Does Python phylogenetic software work for comparative genomics and gene family evolution analysis?▼

Yes, Python phylogenetic software works for comparative genomics. It enables gene family evolution analysis by detecting duplications, identifying orthologs across species, and visualizing annotated evolutionary events.

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