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LeonChaoX
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etetoolkit

Manipulate phylogenetic trees and render publication-quality figures to PDF, SVG, or PNG.

783|65|Updated Feb 27, 2026
Search Tags:#ete3#orthology#phylogenetic trees#tree visualization#taxonomy (ncbi)#robinson-foulds
One-click install
npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill etetoolkit-leonchaox
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: etetoolkit
Source: https://github.com/LeonChaoX/qinyan-academic-skills/tree/main/skills/05-%E7%94%9F%E7%89%A9%E4%BF%A1%E6%81%AF%E4%B8%8E%E5%9F%BA%E5%9B%A0%E7%BB%84%E5%AD%A6/etetoolkit
Command: npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill etetoolkit-leonchaox

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires ete3, PyQt5, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill removes the manual burden of parsing, manipulating, analyzing, and producing publication-ready figures for phylogenetic trees. It helps researchers reliably handle common tree formats and workflows without reinventing custom code each time.

Core Features & Use Cases

  • Tree manipulation & analysis: Load and convert Newick/NHX/PhyloXML/NeXML trees, prune to taxa, reroot (including midpoint), resolve polytomies, compute distances, and compare topologies via Robinson–Foulds.
  • Phylogenetic event analysis: Detect evolutionary events in gene trees, infer orthologs/paralogs, and split gene families around duplication/speciation structure.
  • Taxonomy integration: Download and cache NCBI taxonomy, translate names↔TaxIDs, retrieve lineages, build minimal taxon trees, and annotate tree nodes with taxonomy metadata.
  • Clustering support for hierarchical trees: Link numeric profiles to leaves (via ClusterTree) and evaluate cluster quality metrics like silhouette and Dunn index.
  • Publication-quality visualization: Render trees to PDF/SVG/PNG with configurable styles (rectangular/circular), node styling, and faces; also includes quick CLI visualization helpers.

Quick Start

Ask the AI to visualize a Newick phylogenetic tree as a publication-ready PDF using the ETE Toolkit rendered styles and layouts from the provided skill.

Frequently Asked Questions about etetoolkit

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

FAQPage Schema
How do I visualize a Newick phylogenetic tree as a publication-ready PDF?▼

To visualize phylogenetic trees as publication-ready PDFs, you can load Newick files and apply configurable TreeStyle and NodeStyle layouts to render output in PDF, SVG, or PNG formats.

What is the best way to compare phylogenetic tree topologies using Robinson-Foulds?▼

Comparing phylogenetic tree topologies via Robinson-Foulds is handled by loading multiple tree files and computing batch distances to evaluate topological differences across gene or species trees.

Can I infer orthologs and paralogs from a gene tree?▼

Inferring orthologs and paralogs from a gene tree is supported through phylogenetic event analysis, which detects evolutionary events and splits gene families around duplication and speciation structures.

How do I annotate phylogenetic tree nodes with NCBI taxonomy lineages?▼

Annotating tree nodes with NCBI taxonomy involves downloading and caching the NCBI taxonomy database, translating names to TaxIDs, retrieving lineages, and mapping metadata directly onto tree nodes.

Does ETE3 support loading and converting PhyloXML and NeXML tree formats?▼

ETE3 supports loading and converting PhyloXML and NeXML tree formats, enabling seamless Newick and NHX I/O operations for gene and species tree workflows.

What limitations should I expect when using ETE3 for tree visualization?▼

Limitations of ETE3 for tree visualization include its dependency on PyQt5 for rendering, requiring specific GUI environment configurations to generate publication-quality figures successfully.

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