Can I generate images of my phylogenetic trees?

Absolutely. ETE can render trees in rectangular or circular layouts as PNG, PDF, or SVG files with highly customizable node styles and annotations.

What tree formats does the ETE Toolkit support?

It supports standard formats including Newick, NHX, PhyloXML, and NeXML, allowing for cross-compatibility with most bioinformatics software.

How does NCBI Taxonomy integration work?

The skill facilitates automatic downloading and local caching of the NCBI taxonomy database, enabling quick translation between scientific names and TaxIDs.

Does it support hierarchical clustering results?

Yes, it includes a ClusterTree class specifically designed to link numerical data matrices with hierarchical dendrograms and generate heatmaps.

Can this skill help with orthology detection?

Yes, ETE includes specialized tools for detecting duplication and speciation events to help researchers identify orthologs and paralogs.

ETE Toolkit Phylogenetic Analysis

Name: ETE Toolkit Phylogenetic Analysis
Author: Yezez9

byYezez9

0•

Data Science & ML

Analyzes and visualizes phylogenetic and hierarchical trees with advanced support for evolutionary events and NCBI taxonomy integration.

The ETE Toolkit Skill enables Claude to programmatically manipulate, analyze, and visualize complex phylogenetic trees and hierarchical data. It provides a robust framework for evolutionary biology research, including features for orthology detection, species naming, and seamless integration with the NCBI Taxonomy database. Whether you are building automated phylogenomic pipelines, calculating Robinson-Foulds distances, or generating publication-quality tree diagrams in PDF or SVG formats, this skill streamlines the entire tree exploration workflow with high-performance Python-based utilities.

Key Features

01Multi-format tree manipulation (Newick, NHX, PhyloXML, NeXML)

02High-resolution visualization for PNG, PDF, and SVG exports

03Hierarchical clustering analysis with data matrix and heatmap linking

04Evolutionary event detection for speciation and duplication identification

050 GitHub stars

06Automated NCBI Taxonomy integration and lineage annotation

Use Cases

01Automating the creation of annotated species trees from lists of taxonomic IDs

02Identifying orthologs and paralogs in large-scale gene tree datasets

03Quantifying topological differences between competing trees using Robinson-Foulds metrics

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add yezez9/research-agent etetoolkit

For use in Claude.ai and ChatGPT