etetoolkit

Manipulate, analyze, and visualize phylogenetic trees using the ETE3 library.

557|98|Updated Nov 7, 2025

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

Ready to run

npx skills add https://github.com/jimmc414/Kosmos --skill etetoolkit-jimmc414

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: etetoolkit
Source: https://github.com/jimmc414/Kosmos/tree/main/kosmos-claude-scientific-skills/scientific-skills/etetoolkit
Command: npx skills add https://github.com/jimmc414/Kosmos --skill etetoolkit-jimmc414

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 manipulation, analysis, and visualization, making advanced phylogenomic research accessible.

Core Features & Use Cases

Tree Manipulation: Load, modify, and save trees in various formats (Newick, NHX, etc.).
Phylogenetic Analysis: Detect evolutionary events, identify orthologs, and analyze gene families.
Taxonomy Integration: Connect trees with NCBI taxonomy for annotation.
Visualization: Generate publication-quality tree figures in PDF, SVG, or PNG.
Use Case: Analyze a gene tree to identify orthologous relationships across species, visualize the results, and integrate taxonomic information for a comprehensive report.

Quick Start

Use the etetoolkit skill to load the tree from 'my_tree.nw' and render it as 'output.pdf'.

Frequently Asked Questions about etetoolkit

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

FAQPage Schema

How do I visualize a phylogenetic tree and export it as a PDF?▼

Load a Newick or NHX format phylogenetic tree and render it directly to generate publication-quality PDF, SVG, or PNG visualizations.

What is the best way to identify orthologs across species in a gene tree?▼

Detect evolutionary events and analyze gene families within a loaded phylogenetic tree to identify orthologous relationships across multiple species.

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

Yes, you can connect loaded phylogenetic trees with NCBI taxonomy databases to annotate branches and integrate taxonomic information for evolutionary studies.

Does this approach support loading and saving trees in multiple formats?▼

Yes, phylogenetic tree manipulation supports loading, modifying, and saving trees in multiple formats including Newick and NHX for flexible analysis.

Do I need the ete3 library installed to perform phylogenetic tree manipulation?▼

Yes, the ete3 library is a required dependency to run phylogenetic tree manipulation, analysis, and visualization tasks.