Does it require a local database for NCBI taxonomy?

Upon first use, the skill automatically downloads and caches the NCBI taxonomy database (~300MB) locally to enable fast taxonomic lookups and lineage retrieval.

Can this skill help identify orthologs and paralogs?

Yes, it uses evolutionary event detection (species overlap or tree reconciliation) to distinguish between speciation and duplication events, identifying orthologous relationships.

What tree file formats does the ETE Toolkit support?

The toolkit supports a wide range of standard phylogenetic formats including Newick, NHX, PhyloXML, and NeXML for both reading and writing.

Can I generate images of my phylogenetic trees?

Absolutely. The skill can render trees into publication-ready PDF, SVG, or high-resolution PNG files with fully customizable layouts, colors, and node styles.

ETE Toolkit for Phylogenetics

Name: ETE Toolkit for Phylogenetics
Author: Zehong-Wang

byZehong-Wang

0•

Data Science & ML

Manipulates, analyzes, and visualizes phylogenetic and hierarchical trees for genomic research and clustering analysis.

The ETE (Environment for Tree Exploration) Toolkit skill empowers Claude to handle complex phylogenetic workflows, ranging from basic tree manipulation and format conversion to advanced evolutionary event detection. It provides deep integration with the NCBI Taxonomy database, allowing for automated species annotation and lineage retrieval. Researchers can generate publication-ready visualizations in vector or raster formats, perform orthology and paralogy analysis, and compare tree topologies using standardized metrics like the Robinson-Foulds distance, making it an essential tool for phylogenomics and hierarchical data science.

Key Features

01Advanced tree comparison metrics including Robinson-Foulds and partition analysis

02Evolutionary event detection to identify speciation and duplication nodes

03Publication-quality visualization engine supporting PDF, SVG, and PNG outputs

04Seamless NCBI Taxonomy integration for automated species naming and lineage retrieval

050 GitHub stars

06Comprehensive tree I/O support for Newick, NHX, PhyloXML, and NeXML formats

Use Cases

01Building and annotating species trees using the NCBI taxonomy database

02Generating customized, publication-quality circular or rectangular phylogenetic plots

03Identifying orthologs and paralogs within large-scale gene family trees

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add zehong-wang/kosmos etetoolkit

For use in Claude.ai and ChatGPT

Download Skill