Bio Phylogenomics

Build marker-gene alignments and maximum-likelihood trees, identify closest relatives, and fetch the relative genomes that downstream comparisons need.

Instructions

Tool guides, versions, and verified flags: docs/README.md.

1. Use the literature-derived analysis playbook to choose markers, reference sampling, rooting, and placement strategy for the inferred group.

2. Extract marker genes or SSU rRNA sequences for the queries and references.

3. Validate the marker and reference manifests and write a checksum-gated, fixed-seed plan; inspect run_manifest.json, then rerun with --execute:

   uv run --script skills/bio-phylogenomics/scripts/run_phylogenomics.py \
     markers.tsv --references references.tsv --seed 1729 \
     --tree-tool veryfasttree --threads 4 --out results/bio-phylogenomics/trees