Can this skill help distinguish between orthologs and paralogs?

Yes, it utilizes evolutionary event detection (Species Overlap or tree reconciliation) to identify speciation and duplication events.

Can I use this skill to create charts for research papers?

Absolutely. It generates publication-quality visualizations in PDF, SVG, and PNG formats with customizable node styles and layout functions.

How does the skill handle tree comparison?

It provides automated methods to calculate Robinson-Foulds distances and analyze unique or shared bipartitions between multiple trees.

Does it require a manual download of the NCBI taxonomy database?

No, the skill automatically handles the download and local caching of the ~300MB NCBI taxonomy database upon its first instantiation.

What tree formats does the ETE Toolkit skill support?

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

ETE Toolkit for Phylogenetics

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

byK-Dense-AI

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2,188

Data Science & ML

Manipulates, analyzes, and visualizes phylogenetic and hierarchical trees for genomic research and evolutionary biology.

About

The ETE (Environment for Tree Exploration) Toolkit Skill provides Claude with specialized capabilities for advanced phylogenetic analysis and hierarchical tree exploration. It enables complex operations such as tree manipulation in Newick/NHX formats, evolutionary event detection to distinguish between speciation and duplication, and native integration with the NCBI Taxonomy database for automatic lineage annotation. This skill is ideal for bioinformaticians and data scientists needing to build high-throughput phylogenomic pipelines, calculate Robinson-Foulds distances, or generate publication-quality tree visualizations in vector and raster formats.

Key Features

Evolutionary event detection for identifying orthologs and paralogs
2,188 GitHub stars
Publication-quality visualization supporting PDF, SVG, and PNG output
NCBI Taxonomy integration for automatic species naming and lineage retrieval
Tree I/O and manipulation for Newick, NHX, PhyloXML, and NeXML formats
Hierarchical clustering analysis with data matrix and heatmap integration

Use Cases

Comparing tree topologies and quantifying differences using Robinson-Foulds distances
Automating phylogenomic pipelines from gene trees to ortholog group identification
Generating annotated species trees and taxonomic lineages from lists of taxa

About

Key Features

Evolutionary event detection for identifying orthologs and paralogs
2,188 GitHub stars
Publication-quality visualization supporting PDF, SVG, and PNG output
NCBI Taxonomy integration for automatic species naming and lineage retrieval
Tree I/O and manipulation for Newick, NHX, PhyloXML, and NeXML formats
Hierarchical clustering analysis with data matrix and heatmap integration

Use Cases

Comparing tree topologies and quantifying differences using Robinson-Foulds distances
Automating phylogenomic pipelines from gene trees to ortholog group identification
Generating annotated species trees and taxonomic lineages from lists of taxa