Does this skill require specific Python packages?

Yes, it is designed to work with the 'ete3' library. For advanced visualization features, PyQt5 or Qt5 system dependencies are recommended.

Can I use this skill to identify orthologs and paralogs?

Yes, the skill provides specific methods for evolutionary event detection using species overlap or tree reconciliation to identify orthologous and paralogous sequences.

What visualization layouts are supported?

It supports rectangular and circular tree layouts, and allows for custom styling using NodeStyle and graphical faces (text, charts, heatmaps) exported to PDF, SVG, or PNG.

What file formats does the ETE Toolkit skill support?

It supports standard phylogenetic tree formats including Newick, NHX, PhyloXML, and NeXML for both reading and writing.

How does the NCBI Taxonomy integration work?

The skill facilitates the automatic download and local caching of the NCBI taxonomy database (~300MB), allowing you to translate between scientific names and taxonomic IDs without constant API calls.

ETE Toolkit for Phylogenomics

Name: ETE Toolkit for Phylogenomics
Author: jackspace

byjackspace

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Data Science & ML

Manipulates, analyzes, and visualizes phylogenetic trees and genomic data with the Environment for Tree Exploration (ETE) framework.

The ETE Toolkit Skill equips Claude with the ability to perform complex phylogenetic and hierarchical tree analysis directly within your development environment. It provides a robust set of tools for loading trees in Newick or NHX formats, detecting evolutionary events like duplications and speciations, and integrating seamlessly with the NCBI Taxonomy database for automatic species annotation. Whether you're building phylogenomic pipelines, conducting gene family analysis, or creating publication-quality tree visualizations in SVG or PDF, this skill streamlines the entire bioinformatic workflow by providing standardized implementation patterns for the ETE3 Python library.

Key Features

01Seamless NCBI Taxonomy integration for automatic species-to-taxid translation and lineage retrieval

022 GitHub stars

03Comprehensive tree manipulation including pruning, rooting, and topological modification

04Evolutionary event detection for precise orthology and paralogy identification

05Publication-quality tree visualization with support for PNG, PDF, and SVG formats

06Advanced tree comparison metrics including Robinson-Foulds distance and partition analysis

Use Cases

01Quantifying topological differences between multiple trees to evaluate phylogenetic consistency

02Building automated phylogenomic pipelines for large-scale gene tree analysis and reconciliation

03Generating annotated species trees and high-resolution evolutionary diagrams for scientific publications

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add jackspace/claudeskillz scientific-pkg-etetoolkit

For use in Claude.ai and ChatGPT

Download Skill