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etetoolkit

Analyze and visualize phylogenetic trees using the ete3 library.

Updated May 17, 2026
Search Tags:#gene analysis#evolutionary biology#phylogenetics#tree analysis#tree visualization
One-click install
npx skills add https://github.com/galeep/plugin-place --skill etetoolkit-galeep
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: etetoolkit
Source: https://github.com/galeep/plugin-place/tree/main/plugins/sci-bioinformatics-genomics/skills/etetoolkit
Command: npx skills add https://github.com/galeep/plugin-place --skill etetoolkit-galeep

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill provides tools for analyzing and visualizing phylogenetic trees, streamlining complex phylogenetic analyses and making research more efficient.

Core Features & Use Cases

  • Tree Manipulation: Load, manipulate, and analyze hierarchical tree structures.
  • Phylogenetic Analysis: Detect evolutionary events and identify orthologs and paralogs.
  • Taxonomy Integration: Access and integrate NCBI Taxonomy data.
  • Tree Visualization: Create publication-quality tree visualizations.
  • Clustering Analysis: Analyze hierarchical clustering results with data integration.
  • Use Case: For a researcher analyzing gene trees, this Skill can automatically detect duplications and speciations, extract ortholog groups, and visualize the results.

Quick Start

Load your gene tree file 'gene_tree.nw' into the etetoolkit skill and use the command 'etetoolkit analyze' to perform a comprehensive analysis.

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 detect evolutionary events in a gene tree?▼

Phylogenetic tree visualization and evolutionary event detection are handled by loading your gene tree file for analysis. The toolkit detects duplications and speciations, extracts ortholog groups, and renders publication-quality visualizations using ete3 and matplotlib.

Can I integrate NCBI Taxonomy data into my phylogenetic analysis workflow?▼

Yes, NCBI Taxonomy data integration is supported during phylogenetic analysis using the ncbitaxa package. This maps taxonomic information directly onto hierarchical tree structures for evolutionary biology studies and gene analysis.

What is the best way to extract orthologs and paralogs from a Newick gene tree file?▼

Extract orthologs and paralogs from a Newick gene tree file by running comprehensive phylogenetic analysis. The toolkit identifies ortholog groups and detects speciation events within hierarchical tree structures using the ete3 library.

Do I need pandas and matplotlib to perform hierarchical clustering analysis on tree data?▼

Pandas is required for data integration during hierarchical clustering analysis of tree data, while matplotlib is needed for tree visualization. The ete3 library serves as the core dependency for tree manipulation.

What are the limitations of using ete3 for tree manipulation and clustering analysis?▼

Limitations of using ete3 for tree manipulation and clustering analysis include dependencies on additional packages like ncbitaxa and pandas for full functionality. Proper environment setup is required for biological research workflows.

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