Hop introgression atlas (bundle, 2026-10-14)

Self-contained copy of the introgression atlas and its companion pages from the hop atlas web app. Status of all content: tentative.

• Introgression atlas: NA/EU clade calls per sample and bin, haplotype-resolution levels (subspecies, lineage, cordifolius experimental, WGS variants), Reference selector with per-reference calls, sex-aware ChrX/ChrY, phasing, pedigree lookup, evidence detail
• Badges: every row-label badge and its evidence page (e.g. OSU paternity)
• Phylogeny: pseudo-phylogeny of the full dataset (GBS backbone + placed tips; Zhang 2017 excluded), WGS-only and per-window trees, local affinity heatmap
• Docs: the web app's documentation as it stood when the bundle was made

See CLAUDE.md at the top of the bundle (hop_introgression_atlas_2026-10-14/CLAUDE.md) for what this is, how it was built and how to run it.