etetoolkit

Manipulate phylogenetic trees and detect evolutionary events using ete3.

2|Updated Jun 4, 2026

Search Tags:#bioinformatics #genomics #evolutionary biology #phylogenetics #ncbi taxonomy #tree visualization

Ready to run

npx skills add https://github.com/Lord1Egypt/scientific-agent-toolkit --skill etetoolkit-lord1egypt

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: etetoolkit
Source: https://github.com/Lord1Egypt/scientific-agent-toolkit/tree/main/scientific-skills/etetoolkit
Command: npx skills add https://github.com/Lord1Egypt/scientific-agent-toolkit --skill etetoolkit-lord1egypt

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires ete3, pyqt5, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill addresses the complexity of manipulating, analyzing, and visualizing large-scale phylogenetic trees, which is often a bottleneck in evolutionary biology and genomics research.

Core Features & Use Cases

Tree Manipulation: Perform complex operations like pruning, rerooting, and resolving polytomies on Newick and NHX formats.
Evolutionary Analysis: Detect duplication and speciation events, identify orthologs, and integrate NCBI taxonomy data.
Publication-Quality Visualization: Generate high-resolution PDF, SVG, or PNG figures with custom layouts, node styling, and graphical faces.
Use Case: Researchers can use this to automatically root a set of gene trees, annotate them with NCBI taxonomic lineages, and render publication-ready circular diagrams.

Quick Start

Use the etetoolkit skill to load the file 'tree.nw', perform a midpoint reroot, and render the result as a high-resolution PDF.

Frequently Asked Questions about etetoolkit

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

FAQPage Schema

How do I reroot and visualize a phylogenetic tree for publication?▼

You can reroot and visualize phylogenetic trees by loading Newick or NHX files, applying midpoint rerooting, and rendering high-resolution PDF, SVG, or PNG figures with custom layouts and node styling.

Can I integrate NCBI taxonomy data into my phylogenomic workflow?▼

You can integrate NCBI taxonomy data into phylogenomic workflows to annotate gene trees with taxonomic lineages, identify orthologs, and detect speciation and duplication events.

Does ete3 support complex tree manipulation like pruning and resolving polytomies?▼

Yes, ete3 supports complex tree manipulation including pruning, rerooting, and resolving polytomies on Newick and NHX format trees for advanced evolutionary biology and genomics analysis.

What is the best way to detect evolutionary events in large-scale gene trees?▼

To detect evolutionary events in large-scale gene trees, use phylogenetic tree analysis tools to automatically identify duplication and speciation events while pruning and resolving polytomies.

Do I need pyqt5 to render publication-quality tree visualizations?▼

Yes, pyqt5 is required for rendering publication-quality tree visualizations, as it provides the system dependencies needed for generating high-resolution PDF, SVG, or PNG output.

What are the limitations of using phylogenetic tree manipulation tools for hierarchical clustering?▼

Limitations of using phylogenetic tree manipulation tools include strict dependencies on ete3 and pyqt5 for database operations and rendering, which may constrain hierarchical clustering analysis workflows.