skills/claude-scientific-skills
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Timothy Kassis
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scientific-packages/etetoolkit/SKILL.md
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name: etetoolkit
description: Comprehensive toolkit for phylogenetic and hierarchical tree analysis using the ETE (Environment for Tree Exploration) Python library. This skill should be used when working with phylogenetic trees, gene trees, species trees, clustering dendrograms, or any hierarchical tree structures. Applies to tasks involving tree manipulation (pruning, rerooting, format conversion), evolutionary analysis (orthology detection, duplication/speciation events), tree comparison (Robinson-Foulds distance), NCBI taxonomy integration, tree visualization (PDF, SVG, PNG output), and clustering analysis with heatmaps.
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.
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# ETE Toolkit Skill