Tooluniverse Phylogenetics

This is a batteries-included phylogenetics toolbox built around PhyKIT, Biopython, and DendroPy for multi-gene comparative genomics. It shines when you're working with BUSCO ortholog datasets and need to compute tree quality metrics like treeness, RCV, saturation, or parsimony-informative sites across hundreds of gene families. The scripts handle the tedious parts: paired comparisons between taxonomic groups with Mann-Whitney U tests, group-median ratios versus paired-ortholog ratios, and correct handling of PhyKIT's quirky CLI (parsimony_informative versus parsimony_informative_sites). Rule zero is sensible: check for pre-computed results before re-running six-hour pipelines that produce slightly different numbers due to seed drift. If you're doing evolutionary rate analysis or phylogenomic QC at scale, this eliminates a lot of bash glue and off-by-one errors.

Install to Claude Code

npx -y skills add mims-harvard/tooluniverse --skill tooluniverse-phylogenetics --agent claude-code