What file formats does the ETE Toolkit skill support?

The skill supports standard phylogenetic formats including Newick, NHX, PhyloXML, and NeXML for both reading and writing.

What kind of visualizations can I generate?

You can create publication-quality PDF, SVG, and PNG files with custom node styles, branch support values, and even attached heatmaps or text faces.

Can I use this skill to find orthologs and paralogs?

Yes, it includes specific capabilities for detecting duplication and speciation events to identify orthologous and paralogous gene relationships.

Does this skill require an external taxonomy database?

It uses the NCBITaxa module which automatically downloads and caches a local copy of the NCBI taxonomy database (~300MB) upon first use.

ETE Toolkit for Phylogenetics

Name: ETE Toolkit for Phylogenetics
Author: jimmc414

byjimmc414

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324

Data Science & ML

Analyzes and visualizes phylogenetic trees with support for evolutionary event detection and NCBI taxonomy integration.

About

The ETE Toolkit skill enables Claude to perform advanced phylogenetic and hierarchical tree analysis directly within your development environment. It provides comprehensive tools for manipulating tree structures (Newick, NHX, PhyloXML), detecting evolutionary events like duplications and speciations, and identifying orthologs or paralogs. By integrating with the NCBI Taxonomy database and supporting high-quality rendering in PDF, SVG, and PNG formats, this skill streamlines complex phylogenomic workflows—from raw tree traversal and topology modification to publication-ready visualization and clustering analysis.

Key Features

Seamless NCBI Taxonomy integration for automatic lineage and species annotation
Quantitative tree comparison using Robinson-Foulds and topological distances
324 GitHub stars
Evolutionary event detection for identifying duplications and speciations
Publication-quality visualization with custom node styling and circular layouts
Comprehensive tree manipulation for Newick, NHX, and PhyloXML formats

Use Cases

Building and annotating taxonomic species trees from list of taxa
Performing hierarchical clustering analysis with integrated heatmap visualization
Automating phylogenomic pipelines to identify ortholog and paralog groups

About

Key Features

Seamless NCBI Taxonomy integration for automatic lineage and species annotation
Quantitative tree comparison using Robinson-Foulds and topological distances
324 GitHub stars
Evolutionary event detection for identifying duplications and speciations
Publication-quality visualization with custom node styling and circular layouts
Comprehensive tree manipulation for Newick, NHX, and PhyloXML formats

Use Cases

Building and annotating taxonomic species trees from list of taxa
Performing hierarchical clustering analysis with integrated heatmap visualization
Automating phylogenomic pipelines to identify ortholog and paralog groups