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etetoolkit

Manipulate, analyze, and visualize phylogenetic trees using the ETE3 library.

Updated Mar 10, 2026
Search Tags:#bioinformatics#visualization#evolutionary biology#phylogenetics#tree analysis#ncbi taxonomy
One-click install
npx skills add https://github.com/Yezez9/Research-Agent --skill etetoolkit-yezez9
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: etetoolkit
Source: https://github.com/Yezez9/Research-Agent/tree/main/scientific-skills/etetoolkit
Command: npx skills add https://github.com/Yezez9/Research-Agent --skill etetoolkit-yezez9

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, prune, and reroot trees in various formats (Newick, NHX).
  • Phylogenetic Analysis: Detect evolutionary events (duplication, speciation), identify orthologs/paralogs.
  • Taxonomy Integration: Connect trees with NCBI Taxonomy for annotation and lineage retrieval.
  • Visualization: Generate publication-quality tree figures in PDF, SVG, or PNG.
  • Use Case: Analyze gene duplication events across multiple species to understand evolutionary history and identify orthologous gene families.

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 from a Newick file as a publication-quality figure?▼

To visualize a phylogenetic tree, load your Newick or NHX file and render it directly into publication-quality PDF, SVG, or PNG figures for comparative genomics research.

How can I detect gene duplication and speciation events in a phylogenetic tree?▼

Detect evolutionary events like gene duplication and speciation by analyzing your phylogenetic tree to identify orthologs and paralogs across multiple species.

Can I integrate NCBI Taxonomy data to annotate evolutionary lineages in my tree?▼

Yes, you can integrate NCBI Taxonomy with your tree to retrieve lineage information and annotate nodes for comprehensive phylogenomic analysis.

What tree formats are supported for phylogenetic tree manipulation and analysis?▼

Phylogenetic tree manipulation supports loading, modifying, pruning, and rerooting trees in Newick, NHX, and other standard formats for evolutionary biology research.

What is the best way to analyze orthologous gene families across multiple species?▼

Analyze orthologous gene families by loading a species tree, detecting speciation and duplication events, and comparing evolutionary histories across the loaded taxa.

Does this phylogenetics toolkit work without external dependencies for tree I/O?▼

Yes, this toolkit provides standalone scripts and references for tree I/O, manipulation, and visualization without requiring external dependencies.

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