etetoolkit

Manipulate and analyze phylogenetic trees from Newick data with ete3.

74|5|Updated Dec 10, 2025

Search Tags:#visualization #taxonomy #clustering #phylogenetics #newick #tree analysis

One-click install

npx skills add https://github.com/dralkh/seerai --skill etetoolkit-dralkh

Or copy as Structured Prompt for Agent▼

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

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

ETE Toolkit helps researchers manipulate phylogenetic trees and clustering dendrograms without hand-editing Newick strings or rebuilding visualizations from scratch. It reduces repetitive work in tree cleaning, rooting, pruning, comparison, taxonomy annotation, and figure generation.

Core Features & Use Cases

Tree editing and analysis: Load, traverse, prune, reroot, resolve polytomies, compare topologies, and inspect branch statistics.
Phylogenetic workflows: Detect duplication and speciation events, identify orthologs and paralogs, and work with NCBI taxonomy for species-tree annotation.
Visualization and clustering: Render rectangular or circular trees to PDF, SVG, or PNG, add node faces and styles, and evaluate hierarchical clusters with silhouette and Dunn metrics.
Use case: A researcher can batch-process a folder of gene trees, reroot them at the midpoint, prune to focal taxa, and render publication-ready figures.

Quick Start

Ask the skill to load a Newick tree, summarize its structure, and render a styled phylogenetic figure.

Frequently Asked Questions about etetoolkit

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

FAQPage Schema

How do I visualize and render a phylogenetic tree from a Newick file?▼

You can reroot phylogenetic trees at the midpoint, prune to focal taxa, and resolve polytomies. This streamlines tree cleaning and editing workflows without hand-editing Newick strings.

How does phylogenetic tree comparison work for detecting evolutionary events?▼

To evaluate hierarchical clustering structures, compute silhouette and Dunn metrics. This supports dendrogram evaluation alongside standard phylogenetic tree workflows.

Do I need ete3 to analyze phylogenetic trees and hierarchical clustering structures?▼

Batch-process a folder of gene trees by loading them, rerooting at the midpoint, pruning to focal taxa, and rendering publication-ready figures. This automates repetitive phylogenomic workflows.

What is the best way to batch process gene trees for publication-ready figures?▼

Yes, you can add node faces and custom styles to phylogenetic trees. This allows detailed annotation of evolutionary events and taxa directly within rendered visualizations.