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etetoolkit

Analyze and manipulate phylogenetic trees in Newick and NHX formats.

8|Updated Jan 13, 2026
Search Tags:#bioinformatics#visualization#genomics#evolutionary biology#phylogenetics#tree analysis
One-click install
npx skills add https://github.com/hxk622/TokenDance --skill etetoolkit-hxk622
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: etetoolkit
Source: https://github.com/hxk622/TokenDance/tree/main/backend/app/skills/builtin/scientific/bioinformatics/etetoolkit
Command: npx skills add https://github.com/hxk622/TokenDance --skill etetoolkit-hxk622

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill simplifies complex phylogenetic tree analysis, manipulation, and visualization, making advanced bioinformatics accessible for research and discovery.

Core Features & Use Cases

  • Tree Manipulation: Load, modify, prune, and reroot trees in various formats (Newick, NHX).
  • Phylogenetic Analysis: Detect evolutionary events, identify orthologs/paralogs, and analyze gene families.
  • Taxonomy Integration: Connect trees with NCBI taxonomy for annotation and lineage tracing.
  • Visualization: Generate publication-quality tree figures in PDF, SVG, and PNG formats.
  • Use Case: Analyze a set of gene trees to identify orthologous relationships across different species, then visualize the results with clear annotations.

Quick Start

Use the etetoolkit skill to visualize the phylogenetic tree in 'tree.nw' and save it as 'tree.pdf'.

Frequently Asked Questions about etetoolkit

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

FAQPage Schema
How do I analyze and visualize phylogenetic trees in Newick format?▼

Analyzing and visualizing phylogenetic trees involves loading Newick or NHX files, manipulating the topology through rerooting or pruning, and exporting publication-quality figures in PDF, SVG, or PNG formats.

How do I detect evolutionary events and identify orthologs in a gene tree?▼

Phylogenetic analysis detects evolutionary events and identifies orthologs or paralogs by evaluating gene tree topologies against species relationships to map gene family evolutionary history.

Can I integrate NCBI taxonomy into my phylogenetic tree analysis?▼

Yes, integrating NCBI taxonomy into phylogenetic tree analysis connects tree nodes with the NCBI taxonomy database to enable species annotation and lineage tracing for comparative genomics.

What is the best way to reroot and prune trees for comparative genomics?▼

The best way to reroot and prune trees for comparative genomics uses a programmatic phylogenetic toolkit to precisely manipulate Newick or NHX topologies before running orthology analysis.

Does ete3 support exporting publication-quality tree figures?▼

Yes, ete3 supports exporting publication-quality tree figures by rendering annotated phylogenetic visualizations directly into high-resolution PDF, SVG, and PNG files for research publications.

Why do I need a specialized toolkit for phylogenomics instead of manual tree editing?▼

A specialized toolkit for phylogenomics is necessary because manual tree editing cannot scale to automate orthology analysis, evolutionary event detection, and NCBI taxonomy integration across large gene families.

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