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etetoolkit

Automate phylogenetic tree manipulation, evolutionary analysis, taxonomy integration, and visualization with ete3.

94|11|Updated Mar 26, 2026
Search Tags:#visualization#phylogeny#taxonomy#ete3#phylogenetics
One-click install
npx skills add https://github.com/swaruplab/operon --skill etetoolkit-swaruplab
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: etetoolkit
Source: https://github.com/swaruplab/operon/tree/main/src-tauri/protocols/etetoolkit
Command: npx skills add https://github.com/swaruplab/operon --skill etetoolkit-swaruplab

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Phylogenetic analysis often requires integrating tree manipulation, evolutionary insights, taxonomy, and clear visualizations in a single workflow. ETEToolkit offers a programmable toolkit that unifies these tasks, enabling researchers to manage trees end-to-end from data import to publication-ready figures.

Core Features & Use Cases

  • Tree manipulation and analysis: load, prune, root, traverse, and compare trees; perform topology changes and distance calculations.
  • Phylogenetic analysis: detect duplication/speciation events, extract ortholog groups, and reconcile with species trees.
  • NCBI Taxonomy integration: build taxonomy-aware trees, annotate leaves with taxonomic lineage, and query taxonomy data.
  • Visualization: publication-quality rendering with TreeStyle, NodeStyle, Faces, and various output formats (PDF/SVG/PNG).
  • Clustering and tree comparison: link trees to data matrices, compute silhouette/dunn metrics, and compare trees using RF distances.
  • Workflows and automation: supports end-to-end pipelines for phylogenomic analysis, formatting, and batch processing.

Quick Start

Load a gene tree with an alignment and visualize it.

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 publication-ready PDF?▼

You can visualize phylogenetic trees and render publication-quality figures using TreeStyle, NodeStyle, and Faces, exporting directly to PDF, SVG, or PNG formats. This toolkit supports advanced layout customization for large-scale tree visualization.

What is the best way to detect ortholog groups and speciation events in a gene tree?▼

Detecting ortholog groups and duplication or speciation events is handled by comparing gene trees against species trees. This phylogenetic analysis toolkit automates topology reconciliation to accurately extract evolutionary relationships.

Can I annotate phylogenetic tree leaves with taxonomic lineage from NCBI?▼

Yes, you can annotate trees with NCBI Taxonomy integration. By using the NCBITaxa class, you can build taxonomy-aware trees, annotate leaves with full taxonomic lineages, and query taxonomy data directly.

How do I compare phylogenetic tree topologies and calculate Robinson-Foulds distances?▼

You can compare phylogenetic tree topologies by computing Robinson-Foulds distances. The toolkit enables direct tree comparison and allows linking trees to data matrices to compute silhouette and dunn clustering metrics.

Does ete3 support batch processing for phylogenomic workflows?▼

Yes, ete3 supports end-to-end phylogenomic workflows and batch processing. You can automate comprehensive pipelines for tree manipulation, formatting, and evolutionary analysis across multiple large trees.

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