Bio Protein Clustering Pangenome

Cluster proteins into orthogroups and derive pangenome matrices.

Instructions

Tool guides and versions: docs/README.md.

1. After clustering, build and validate the complete small-to-large comparison bundle with:

   uv run --script skills/bio-protein-clustering-pangenome/scripts/build_pangenome_artifacts.py \
     orthogroups.tsv --genomes genomes.tsv --marker-catalog marker_catalog.tsv \
     --marker-hits marker_hits.tsv --ncrna ncRNA_census.tsv \
     --out results/bio-protein-clustering-pangenome