Etetoolkit

If you're working with phylogenetic trees or doing any serious evolutionary analysis, this gives Claude direct access to the ETE toolkit. It handles the full workflow: reading Newick and NHX formats, detecting duplication and speciation events, identifying orthologs and paralogs, and rendering publication-quality visualizations as PDF or SVG. The NCBI taxonomy integration is genuinely useful for annotating trees with lineage information. The included command-line scripts for tree operations and visualization mean you can get results without writing Python every time. It's GPL-licensed, so factor that into your project's compliance requirements.

Install to Claude Code

npx -y skills add k-dense-ai/scientific-agent-skills --skill etetoolkit --agent claude-code