Etetoolkit

If you're doing phylogenetics or working with evolutionary trees, this wraps the ETE3 toolkit for tree manipulation and analysis. You get Newick/NHX parsing, tree traversal and pruning, orthology detection through evolutionary event analysis, and NCBI taxonomy integration that auto-downloads the database locally. The visualization pipeline outputs publication-ready PDFs and SVGs with custom node styling and annotation faces. It includes helper scripts for quick operations like midpoint rooting and format conversion. The real value is in gene family analysis where you can detect duplication events, split trees into ortholog groups, and link trees to sequence alignments. Beats writing custom tree parsers when you need to do serious phylogenomic work beyond what basic Newick libraries offer.

Install to Claude Code

npx -y skills add davila7/claude-code-templates --skill etetoolkit --agent claude-code