Bio Phylogenomics

Build marker gene alignments and phylogenetic trees.

Instructions

Tool guides and versions: docs/README.md.

1. Validate marker/reference manifests and create a checksum-gated, fixed-seed execution plan:

   uv run --script skills/bio-phylogenomics/scripts/run_phylogenomics.py \
     markers.tsv --references references.tsv --seed 1729 \
     --out results/bio-phylogenomics
   # Inspect run_manifest.json, then add --execute.