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etetoolkit

Automates phylogenetic tree analysis and visualization using the ETE toolkit.

6|Updated Dec 30, 2025
Search Tags:#bioinformatics#visualization#taxonomy#ncbi#ete3#phylogenetics#phylogenetic-tree
One-click install
npx skills add https://github.com/pur3v4d3r/pur3-pkb-codebase --skill etetoolkit-pur3v4d3r
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: etetoolkit
Source: https://github.com/pur3v4d3r/pur3-pkb-codebase/tree/main/.claude/skills/__scientific-skills/etetoolkit
Command: npx skills add https://github.com/pur3v4d3r/pur3-pkb-codebase --skill etetoolkit-pur3v4d3r

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

ETE Toolkit provides an integrated, programmable environment to load, manipulate, analyze, annotate, and visualize phylogenetic trees, enabling researchers to derive insights from evolutionary relationships with reproducible workflows.

Core Features & Use Cases

  • Tree manipulation and analysis (load from Newick/NHX, prune, root, traverse, compute distances)
  • Evolutionary event detection (duplication/speciation identification) and orthology inference
  • Taxonomy integration via NCBITaxa to annotate leaves, build lineages, and connect trees to taxonomic data
  • High-quality visualizations with publication-ready outputs (PDF/SVG/PNG), including circular layouts and advanced faces

Quick Start

Load a gene tree with an alignment file and render a publication-ready visualization.

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?▼

To visualize a phylogenetic tree for publication, load your tree data from Newick or NHX formats and render it directly into high-quality PDF, SVG, or PNG outputs using the integrated ETE toolkit environment.

What is the best way to annotate phylogenetic tree leaves with NCBI taxonomy data?▼

Annotating phylogenetic tree leaves with NCBI taxonomy data uses NCBITaxa integration to connect tree leaves to taxonomic records. This builds lineages and connects your phylogenetic trees directly to standardized taxonomic data.

Can I infer orthology and detect evolutionary events like duplication in a phylogenetic tree?▼

Yes, you can infer orthology and detect evolutionary events within phylogenetic trees. The toolkit identifies duplication and speciation events by analyzing tree structures to derive insights from evolutionary relationships.

Does etetoolkit work with Newick and NHX formats for tree manipulation?▼

Yes, it works with Newick and NHX formats for tree manipulation. You can load, prune, root, traverse, and compute distances on trees using these formats, ensuring interoperability across phylogenomic research workflows.

How do I load a gene tree with an alignment file for evolutionary analysis?▼

Loading a gene tree with an alignment file uses Python-based scripting interfaces supporting Tree, PhyloTree, and ClusterTree objects. This automates comprehensive phylogenetic analysis and visualization workflows reproducibly.

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