skills/claude-scientific-skills
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Fix descriptions to adhere to character limits

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Timothy Kassis
2025-10-21 09:33:30 -07:00
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scientific-packages/etetoolkit/SKILL.md
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name: etetoolkit
description: "Expert toolkit for phylogenetic and hierarchical tree analysis using ETE (Environment for Tree Exploration). Use this skill for any tree-related bioinformatics tasks including phylogenetic trees, gene trees, species trees, clustering dendrograms, taxonomic hierarchies, or evolutionary analysis. Key applications: tree manipulation (pruning, rerooting, format conversion between Newick/NHX/PhyloXML/NeXML), evolutionary event detection (orthology/paralogy identification, duplication/speciation events), tree comparison and topology analysis (Robinson-Foulds distances, consensus trees), NCBI taxonomy integration (taxonomic ID lookup, lineage retrieval, species tree construction), tree visualization and publication figures (PDF/SVG/PNG output, custom styling, interactive GUI), clustering analysis with heatmaps and validation metrics, sequence alignment integration, gene family analysis, and phylogenomic pipelines. Handles Newick formats 0-100, supports large trees with memory-efficient iteration, provides command-line tools for batch processing, and integrates with biological databases for comprehensive phylogenetic analysis workflows."
description: "Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics."
---
# ETE Toolkit Skill