What is the Robinson-Foulds distance used for?

It is a standard metric supported by the skill to quantify and compare the topological differences between two phylogenetic trees.

What file formats does the ETE Toolkit support?

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

Can I create visualizations for scientific papers?

Absolutely. The skill provides patterns for generating high-resolution PDF, SVG, and PNG images with custom node styles, labels, and graphical annotations.

Does it require a local database for NCBI taxonomy?

Upon first initialization, the NCBITaxa module automatically downloads and caches the NCBI taxonomy database (~300MB) locally to enable fast queries.

Can this skill identify orthologs and paralogs?

Yes, it uses evolutionary event detection strategies like species overlap or tree reconciliation to distinguish between duplication and speciation events.

ETE Phylogenetic Toolkit

Name: ETE Phylogenetic Toolkit
Author: Sologa

bySologa

Data Science & ML

Provides comprehensive tools for phylogenetic tree manipulation, evolutionary analysis, and high-quality biological data visualization.

About

The ETE (Environment for Tree Exploration) Toolkit skill empowers Claude to perform advanced phylogenomic research and hierarchical tree analysis. It enables seamless manipulation of Newick, NHX, and PhyloXML formats, automates evolutionary event detection for orthology and paralogy identification, and integrates directly with the NCBI Taxonomy database for automated lineage retrieval. Whether you are conducting clustering analysis or generating publication-ready tree visualizations in PDF or SVG, this skill provides the programmatic patterns and domain-specific logic needed for professional bioinformatics workflows.

Key Features

Comprehensive tree manipulation including pruning, rooting, and format conversion
Native NCBI Taxonomy integration for taxonomic ID translation and lineage annotation
Evolutionary event detection to automatically identify orthologs and paralogs
Publication-quality visualization support for PDF, SVG, and PNG formats
Advanced clustering analysis with silhouette coefficient and Dunn index validation
0 GitHub stars

Use Cases

Generating annotated species trees with taxonomic metadata for scientific publications
Comparing topological differences between multiple trees using Robinson-Foulds distances
Building automated phylogenomic pipelines from gene trees to ortholog groups

About

Key Features

Comprehensive tree manipulation including pruning, rooting, and format conversion
Native NCBI Taxonomy integration for taxonomic ID translation and lineage annotation
Evolutionary event detection to automatically identify orthologs and paralogs
Publication-quality visualization support for PDF, SVG, and PNG formats
Advanced clustering analysis with silhouette coefficient and Dunn index validation
0 GitHub stars

Use Cases

Generating annotated species trees with taxonomic metadata for scientific publications
Comparing topological differences between multiple trees using Robinson-Foulds distances
Building automated phylogenomic pipelines from gene trees to ortholog groups