What tree formats does the ETE Toolkit skill support?

It supports standard phylogenetic formats including Newick, NHX, PhyloXML, and NeXML for both input and output operations.

Can I use this skill to identify orthologs and paralogs?

Yes, the skill utilizes evolutionary event detection algorithms, such as species overlap or tree reconciliation, to distinguish between duplication and speciation events.

Can I generate high-resolution images for papers?

Absolutely. The toolkit supports rendering trees as publication-ready SVG and PDF vector files, as well as high-DPI PNG images with custom styling.

How does the NCBI Taxonomy integration work?

The skill automatically manages the download and local caching of the NCBI taxonomy database, allowing for fast translation between taxids, scientific names, and full lineages.

ETE Toolkit for Phylogenetics

Name: ETE Toolkit for Phylogenetics
Author: lifangda

bylifangda

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Data Science & ML

Manipulates, analyzes, and visualizes phylogenetic and hierarchical trees for biological research and genomic data.

About

The ETE (Environment for Tree Exploration) Toolkit skill provides Claude with specialized capabilities for phylogenomic analysis and hierarchical tree exploration. It enables advanced tree manipulation—including I/O for Newick, NHX, and PhyloXML formats—evolutionary event detection for identifying orthologs and paralogs, and seamless integration with the NCBI Taxonomy database. This skill is essential for researchers needing to perform complex tasks like tree reconciliation, Robinson-Foulds distance calculations, and the generation of publication-quality tree visualizations in vector or raster formats.

Key Features

Publication-quality tree visualization with circular and rectangular layout support
Comprehensive tree manipulation including pruning, rooting, and format conversion
Automated NCBI Taxonomy integration for lineage retrieval and species annotation
Evolutionary event detection to identify duplication and speciation events
Statistical tree comparison using Robinson-Foulds and partition analysis
16 GitHub stars

Use Cases

Performing large-scale taxonomic database queries and tree reconciliation for species mapping
Automating phylogenomic pipelines from gene trees to ortholog identification
Generating high-resolution, data-annotated tree diagrams for scientific publications

About

Key Features

Publication-quality tree visualization with circular and rectangular layout support
Comprehensive tree manipulation including pruning, rooting, and format conversion
Automated NCBI Taxonomy integration for lineage retrieval and species annotation
Evolutionary event detection to identify duplication and speciation events
Statistical tree comparison using Robinson-Foulds and partition analysis
16 GitHub stars

Use Cases

Performing large-scale taxonomic database queries and tree reconciliation for species mapping
Automating phylogenomic pipelines from gene trees to ortholog identification
Generating high-resolution, data-annotated tree diagrams for scientific publications