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Update SKILL.md files to add double quotation marks for all skills, ensuring clarity and consistency across all entries.

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Haoxuan "Orion" Li
2025-10-20 20:51:50 -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: "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