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.

skills.sh installs: 365
GitHub stars: 1.8K
last updated: Aug 21, 2026

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Install

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

Installs into .claude/skills of the current project.

Files

Phylogenetics and Sequence Analysis

Four traps that produce a confidently wrong number

Each of these was observed producing a wrong answer while the correct guidance was already present further down this file. Check them before you answer.

PhyKIT prints more than one column, and for saturation the two conventions disagree — state which you used. phykit saturation prints saturation <TAB> |saturation-1|. Its own --help is explicit: "The first value is the saturation value and the second column is the absolute value of saturation minus 1." But several published analyses (and some reference answers derived from them) report the second column as "the saturation value". The two always sum to 1.0000, which is the tell that you may be looking at the wrong one — on the fungal scogs set the medians are 0.39 (col 1) and 0.61 (col 2).

So: follow phykit and use column 1 unless the question or source defines saturation the other way, and say in your answer which column you read. Do not silently pick the one that looks closer to an expected number.

SKILL.md on GitHub

Details

Repository: github.com/mims-harvard/tooluniverse
Categories: DevOps & CI/CD, Git & Pull Requests, Sales & Marketing
First seen: Jun 3, 2026