What tree file formats can this skill handle?

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

Does it support publication-quality graphics?

Yes, it can render trees to PDF and SVG vector formats, as well as high-DPI PNG files, with full control over node styles, colors, and layouts.

Can I use this for non-biological data?

Yes, while designed for phylogenetics, it is excellent for any hierarchical clustering analysis, dendrogram manipulation, or tree-based data structures.

How does it identify orthologs?

It uses evolutionary event detection (speciation vs. duplication) based on species overlap or tree reconciliation algorithms to distinguish orthologs from paralogs.

How does it integrate with NCBI Taxonomy?

It automatically manages a local SQLite copy of the NCBI taxonomy database, allowing you to translate between TaxIDs and scientific names or retrieve full lineages.

ETE Phylogenetic Toolkit

Name: ETE Phylogenetic Toolkit
Author: Activer007

byActiver007

0•

Data Science & ML

Manipulates, analyzes, and visualizes phylogenetic and hierarchical trees with seamless NCBI taxonomy integration.

The ETE Toolkit Skill empowers Claude to perform complex phylogenomic analyses and tree manipulations directly within your development environment. It provides specialized tools for reading and writing multiple tree formats (Newick, NHX, PhyloXML), detecting evolutionary events like speciation and duplication, and identifying orthologs and paralogs. By integrating with the NCBI Taxonomy database and offering robust visualization options for PDF, SVG, and PNG, it streamlines bioinformatics workflows, clustering analysis, and comparative genomics research.

Key Features

01Tree manipulation and I/O support for Newick, NHX, and PhyloXML formats

02Topological tree comparison using Robinson-Foulds distances

03Automated NCBI Taxonomy database integration and lineage retrieval

04Publication-quality tree visualization in vector and raster formats

05Evolutionary event detection for orthology and paralogy identification

060 GitHub stars

Use Cases

01Generating annotated species trees from taxonomic IDs or scientific names

02Automating gene family analysis and ortholog detection pipelines

03Creating high-resolution, customized tree visualizations for scientific publications

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add activer007/ordinary-claude-skills etetoolkit

For use in Claude.ai and ChatGPT

Download Skill