What visualization options are available?

You can render trees in rectangular or circular layouts as PDF, SVG, or PNG files with fully customizable node styles and graphical faces.

What tree formats does the ETE Toolkit skill support?

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

Can I use this skill to identify orthologs and paralogs?

Yes, it includes specific implementations for evolutionary event detection to distinguish between duplication and speciation events.

Does it support tree comparison metrics?

Yes, it can calculate Robinson-Foulds (RF) distances and perform partition analysis to compare topological differences between trees.

How does the NCBI Taxonomy integration work?

The skill facilitates the automatic download and local caching of the NCBI taxonomy database (~300MB) for fast lookups and lineage retrieval.

ETE Toolkit for Phylogenetics

Name: ETE Toolkit for Phylogenetics
Author: x-cmd

byx-cmd

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データサイエンスとML

Manipulates, analyzes, and visualizes phylogenetic trees with support for evolutionary event detection and NCBI taxonomy integration.

概要

The ETE Toolkit Skill empowers AI coding agents to perform sophisticated phylogenetic and hierarchical tree analysis within your development environment. It provides comprehensive patterns for tree manipulation in formats like Newick, NHX, and PhyloXML, as well as specialized tools for detecting evolutionary events such as duplications and speciations. With native NCBI Taxonomy integration and robust visualization capabilities for generating publication-quality PDF and SVG files, this skill is essential for bioinformatics workflows, phylogenomic research, and complex hierarchical data clustering.

主な機能

Comprehensive tree I/O and topological manipulation including pruning, rooting, and traversal.
Publication-quality tree visualization in PDF, SVG, and PNG formats with custom styling.
8 GitHub stars
Evolutionary event detection to accurately identify orthologs and paralogs in gene trees.
Advanced tree comparison metrics including Robinson-Foulds distance and partition analysis.
Seamless NCBI Taxonomy integration for automatic species annotation and lineage retrieval.

ユースケース

Generating high-resolution, customized tree visualizations for biological research and publications.
Building and annotating species trees using real-time data from the NCBI Taxonomy database.
Automating phylogenomic pipelines from raw gene trees to annotated ortholog groups.

概要

主な機能

Comprehensive tree I/O and topological manipulation including pruning, rooting, and traversal.
Publication-quality tree visualization in PDF, SVG, and PNG formats with custom styling.
8 GitHub stars
Evolutionary event detection to accurately identify orthologs and paralogs in gene trees.
Advanced tree comparison metrics including Robinson-Foulds distance and partition analysis.
Seamless NCBI Taxonomy integration for automatic species annotation and lineage retrieval.

ユースケース

Generating high-resolution, customized tree visualizations for biological research and publications.
Building and annotating species trees using real-time data from the NCBI Taxonomy database.
Automating phylogenomic pipelines from raw gene trees to annotated ortholog groups.