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etetoolkit

Analyze phylogenetic trees with Python's ete3 library and NCBITaxa taxonomy annotations.

21|1|Updated Mar 19, 2026
Search Tags:#taxonomy#ete3#phylogenetics#phylogenomics#gene trees
One-click install
npx skills add https://github.com/OwnLabAI/ownlab --skill etetoolkit-ownlabai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: etetoolkit
Source: https://github.com/OwnLabAI/ownlab/tree/main/mart/skills/scientific-skills/etetoolkit
Command: npx skills add https://github.com/OwnLabAI/ownlab --skill etetoolkit-ownlabai

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Phylogenetic tree analysis can be complex and fragmented; ETE Toolkit provides an integrated set of tools to manipulate trees, perform evolutionary-event detection, annotate with taxonomy, and generate publication-ready visualizations within a single workflow.

Core Features & Use Cases

  • Tree manipulation and analysis: load, prune, root, traverse, compare, and visualize trees in multiple formats (Newick, NHX, PhyloXML, NeXML).
  • Evolutionary analysis and taxonomy integration: detect duplication/speciation events, identify orthologs/paralogs, and annotate trees using NCBI taxonomy or custom taxonomies.
  • End-to-end workflows for phylogenomics: build ortholog groups, annotate leaves with species data, and generate publication-ready figures, reports, and data products.
  • Use Case: A researcher loads a gene family tree, detects evolutionary events, links taxonomic context, and produces annotated trees and summary statistics.

Quick Start

Install the ete3 library, load a gene tree with optional alignment, configure species naming, and run the basic evolutionary-event workflow.

Frequently Asked Questions about etetoolkit

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

FAQPage Schema
How do I detect duplication and speciation events in a phylogenetic tree?▼

You can detect duplication and speciation events in a phylogenetic tree by loading a gene family tree and running an evolutionary-event workflow. This requires configuring species naming to accurately identify orthologs and paralogs.

Can I annotate phylogenetic trees with NCBI taxonomy data?▼

Yes, you can annotate phylogenetic trees with NCBI taxonomy data using NCBITaxa integration. This allows you to link taxonomic context to tree leaves and apply custom taxonomies for comprehensive phylogenomic analysis.

What formats are supported for loading and visualizing phylogenetic trees?▼

Supported formats for loading and visualizing phylogenetic trees include Newick, NHX, PhyloXML, and NeXML. You can load, prune, root, traverse, compare, and generate publication-ready visualizations across these formats.

Do I need Python and the ete3 library to perform phylogenomic analysis and generate publication-ready figures?▼

Yes, you need Python and the ete3 library to perform phylogenomic analysis and generate publication-ready figures. This environment supports building ortholog groups, annotating leaves with species data, and producing summary statistics.

What is the best way to build ortholog groups and annotate leaves with species data?▼

The best way to build ortholog groups and annotate leaves with species data is to use an end-to-end phylogenomic workflow. This enables you to load a gene tree, configure species naming, and generate annotated trees with summary reports.

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