What tree formats does the ETE Toolkit skill support?

It supports a wide range of formats including Newick, NHX, PhyloXML, and NeXML for both reading and writing hierarchical tree data.

Does it require an external database for taxonomy?

The skill integrates with the NCBI Taxonomy database; upon first use, it can automatically download and cache the database locally for rapid lineage retrieval.

Is it suitable for non-biological hierarchical data?

Yes, while designed for biology, the ClusterTree and standard Tree classes are highly effective for any hierarchical clustering or dendrogram analysis in general data science.

Can I generate publication-quality images of the trees?

Absolutely. It supports rendering trees to PDF, SVG, and high-resolution PNG formats with fully customizable layouts, colors, and node annotations.

Can this skill help identify orthologs and paralogs?

Yes, it includes specialized patterns for detecting evolutionary events like duplications and speciations to accurately distinguish between orthologs and paralogs.

ETE Toolkit for Phylogenetics

Name: ETE Toolkit for Phylogenetics
Author: K-Dense-AI

byK-Dense-AI

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3,718

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数据科学与机器学习

Manipulates, analyzes, and visualizes phylogenetic trees and hierarchical data using the Environment for Tree Exploration (ETE) framework.

The ETE Toolkit skill empowers Claude to perform complex phylogenetic and phylogenomic tasks, ranging from basic tree manipulation (Newick/NHX) to advanced evolutionary event detection. It integrates seamlessly with the NCBI Taxonomy database for automatic annotation and supports publication-quality visualization in multiple formats. Whether you're identifying orthologs, calculating Robinson-Foulds distances, or performing hierarchical clustering analysis, this skill provides the domain-specific logic and code patterns required for high-level biological data science and computational biology workflows.

主要功能

01Topological comparison metrics including Robinson-Foulds distance calculations

02Comprehensive tree manipulation and format conversion (Newick, NHX, PhyloXML, NeXML)

03Evolutionary event detection for automated orthology and paralogy identification

043,718 GitHub stars

05Publication-quality visualization with custom node styling and graphical faces

06Seamless NCBI Taxonomy integration for species naming and lineage retrieval

使用场景

01Annotating species trees with taxonomic metadata and evolutionary lineages

02Performing hierarchical clustering analysis on numerical data matrices with heatmap visualization

03Building automated phylogenomic pipelines for large-scale gene family analysis

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add k-dense-ai/claude-scientific-skills etetoolkit

For use in Claude.ai and ChatGPT

Download Skill