etetoolkit

Manipulate and analyze phylogenetic trees in Newick, NHX, PhyloXML, and NeXML formats.

52|6|Updated Nov 24, 2025

Search Tags:#visualization #phylogenetics #ete toolkit #newick #nhx

Ready to run

npx skills add https://github.com/ovachiever/droid-tings --skill etetoolkit-ovachiever

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: etetoolkit
Source: https://github.com/ovachiever/droid-tings/tree/main/skills/etetoolkit
Command: npx skills add https://github.com/ovachiever/droid-tings --skill etetoolkit-ovachiever

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

ETE Toolkit enables manipulation, analysis, and visualization of phylogenetic trees, integrating with NCBI taxonomy and various formats for research and education.

Core Features & Use Cases

Tree manipulation (load, prune, root, reroot, traverse)
Tree analysis (distances, RF distance, monophyly checks)
Visualization (3D/2D layouts, faces, custom styles)
NCBI taxonomy integration via ETE's NCIBTaxa

Quick Start

Load a Newick tree, prune to a subset, and render rooted output with a basic visualization.

Frequently Asked Questions about etetoolkit

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

FAQPage Schema

How do I load and visualize a phylogenetic tree from Newick format?▼

Load Newick format trees using ETE Toolkit's tree I/O functions, then render them with configurable 2D/3D layouts and custom styles via TreeStyle to produce publication-quality visualizations for research workflows.

Can I work with multiple phylogenetic formats like NHX, PhyloXML, and NeXML in the same workflow?▼

ETE Toolkit supports loading, writing, and converting between Newick, NHX, PhyloXML, and NeXML formats, enabling seamless format transitions across phylogenetic analysis pipelines.

How do I detect evolutionary events and infer orthology in phylogenetic trees?▼

Use ETE Toolkit's evolutionary event detection and orthology inference functions to automatically identify duplication, speciation, and loss events, then extract orthologous gene groups across species.

What tree manipulation operations does the toolkit support for topology modification?▼

Tree traversal and topology modification operations include loading, pruning, rooting, rerooting, and custom node manipulation to reshape phylogenetic structures for downstream analysis.

How do I integrate NCBI taxonomy data into my phylogenetic analysis?▼

Link phylogenetic trees to NCBI taxonomy via ETE's NCBITaxa integration to annotate species names, validate taxonomic relationships, and enrich tree visualizations with standardized nomenclature.

Can I compute distances and test monophyly in phylogenetic trees?▼

Calculate pairwise distances, Robinson-Foulds distance metrics, and perform monophyly tests to quantify tree topology differences and validate evolutionary relationships.