bio-interdomain-hgtlisted

# Bio Interdomain HGT Detect, polarize, and confirm horizontal gene transfer between a query genome (virus, MAG, isolate, or bin) and other domains of life. Built for the common asymmetric case where the query is well annotated but the comparison set is genome-only (proteins missing). Pairs with `/bio-annotation` (homology/taxonomy), `/bio-phylogenomics` (trees), `/bio-viromics` (viral classification), and `/bio-fasta-database-curator` (building the arbiter database). ## Instructions Run the steps in order; capture outputs and provenance at each step. Steps 0 (database gate) and 5 (frame-aware context guard on eukaryotic DNA) are the ones most often skipped and most often responsible for wrong conclusions. Use the versioned evidence driver after the homology, context, and tree tools have produced their normalized TSVs: ```bash uv run --no-project python skills/bio-interdomain-hgt/scripts/run_hgt_evidence.py \ forward_hits.tsv --arbiter-hits arbiter_hits.tsv --reciprocal reciprocal.tsv \ --context context.tsv --trees trees.tsv --sampling-depth sampling_depth.tsv \ --databases databases.json --hypotheses hypotheses.tsv --reflections reflections.tsv \ --query-domain ncldv --out results/bio-interdomain-hgt ``` The driver checksum-verifies the comprehensive arbiter, labels, and comparison collection; applies homology, reciprocal-best-hit, direction, frame-aware context, and phylogeny gates; normalizes confirmed candidates by lineage sampling depth; and requires a hyp