Is there support for tree comparison?

Definitely. It includes tools to calculate Robinson-Foulds distances and analyze topological differences between multiple trees.

Can Claude generate tree images using this skill?

Yes, Claude can utilize scripts to render trees as PDF, SVG, or PNG files, including custom styles, colors, and heatmap faces.

What tree formats does the ETE Toolkit skill support?

It supports standard formats including Newick, NHX, PhyloXML, and NeXML for both reading and writing.

Can I use this skill to identify orthologs?

Yes, it includes evolutionary event detection to distinguish between speciation and duplication events, enabling automated orthology identification.

How does the NCBI Taxonomy integration work?

The skill can automatically download and cache the NCBI taxonomy database, allowing you to translate between TaxIDs, scientific names, and full lineages.

ETE Phylogenetic Toolkit

Name: ETE Phylogenetic Toolkit
Author: Microck

byMicrock

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Data Science & ML

Manipulates, analyzes, and visualizes phylogenetic and hierarchical tree structures for phylogenomics and clustering research.

The ETE (Environment for Tree Exploration) Toolkit skill empowers Claude to handle complex biological tree data, including Newick and NHX formats. It provides robust capabilities for tree manipulation, evolutionary event detection (speciation/duplication), and seamless integration with the NCBI Taxonomy database. Whether you are identifying orthologs, performing clustering analysis with data heatmaps, or generating publication-quality SVG/PDF visualizations, this skill streamlines the entire phylogenomic research pipeline directly within your coding environment.

Key Features

01Tree manipulation and I/O for Newick, NHX, and PhyloXML formats

02Evolutionary event detection to identify orthologs and paralogs

03Automated NCBI Taxonomy integration for lineage and taxid retrieval

04High-quality tree visualization in PDF, SVG, and PNG formats

05Hierarchical clustering analysis with integrated data matrix heatmaps

0681 GitHub stars

Use Cases

01Generating publication-ready phylogenetic tree diagrams with custom annotations

02Building automated phylogenomic pipelines for gene family analysis

03Quantifying topological differences between trees using Robinson-Foulds distances

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add microck/ordinary-claude-skills etetoolkit

For use in Claude.ai and ChatGPT

Download Skill