Phylogeny view (`:8900/phylogeny/`)

Status: tentative. Added 2026-10-10 (PI: "make it a view on 8900 and add it to the index").

What is served

Page: /phylogeny/ = scratch_plots/phylogeny → /data/hop_data/hop_atlas/phylogeny/ (not in git; about 2.8 MB).
index.html, phylo.js: plain JS + SVG, no external libraries.
report.html: the analysis report, rendered from sync/2026-10-10/hop_phylogeny/REPORT.md.
data/main.json: 753 tips (labels, cohort, assay, colour classes, highlight kind, founders, placement stability, same-plant aliases, introgression-atlas key and badges) and the display tree (midpoint display root, bootstrap as an edge property).
data/wgs_trees.json: WGS joint-call BIONJ and IQ-TREE ML trees (30 plants), the catalogue-site WGS-only BIONJ tree, and 100 local BIONJ trees (91 windows of 25 Mb + 9 whole chromosomes; WGS plants only).
data/affinity.json: nearest WGS reference group, margin and the five group distances per plant and window (743 drawn tips).
Page source (git): hop_atlas/tools/phylogeny_view/. Builder: hop_atlas/tools/build_phylogeny_view.py.

What it offers

Main tree: circular or linear layout, wheel zoom and drag pan.
Highlighted tips are marked and labelled as in the report's highlight figures: founders = black star, assemblies = orange diamond, wild/feral = coloured by subspecies label.
Colour rings: subspecies label, assay, cohort, atlas category.
Bootstrap dots (threshold 50/70/95 %, optional values).
Collapsed mode: maximal clades of at most N tips, named by the founders, wild groups and assemblies they contain.
Tips can be coloured by local affinity in the window chosen with the slider.
Search: case-, accent- and punctuation-insensitive, over names, run ids, cohorts and the labels of other libraries of the same plant; falls back to all-words and edit distance ≤ 2. Highlights matches and zooms to them. ?q=<text> in the URL searches on load.
Hover / click: name, cohort, assay, labels and placement stability for placed tips. Clicking a tip selects it, links to its introgression-atlas row (/introgression_atlas/?sample=<key>) and its evidence badges, and adds it to the heatmap.
WGS-only trees: the 3 whole-genome trees, or a per-chromosome / per-window tree selector.
Local affinity heatmap: rows = highlighted tips, clicked tips, search matches or all tips; 25 Mb windows; the slider (or a click on a column) picks the window.
Footer: method, caveats, TENTATIVE, the report link and the note that Zhang 2017 is removed.

Rebuild

python3 hop_atlas/tools/build_phylogeny_view.py          # writes /data/hop_data/hop_atlas/phylogeny, creates the scratch_plots link if missing

The page is live as soon as it is written (new component, nothing else serves these files). Re-run after any re-run of the phylogeny pipeline (sync/2026-10-10/hop_phylogeny/PIPELINE.sh) or after an edit to the page source.

Inputs: /data/hop_data/hop_phylogeny/{trees,wgs_joint}/ (combined.nwk, plants.tsv, local_trees.pkl, local_affinity.tsv.gz, WGS joint trees), the report's tables/ (full_tree_tips, tip_colour_classes, highlighted_tips, founders_found_missing, sample_table) and the WGS joint-call sample table (sync/2026-10-10/wgs_subspecies_variants/tables/W00_samples.tsv). The builder also looks in sync_archive/ once those folders are archived. Atlas keys and badges come from the served introgression atlas (multires/atlas_samples_5Mb.json, sexchrom/atlas_sexchrom.json).

Rules kept by the builder: - Zhang 2017 HapMap is never drawn: the builder refuses a tree containing Zhang tips and drops Zhang libraries from aliases and affinity. - The root is a midpoint display root, labelled as such. Bootstrap support is carried as an edge property through the re-rooting.

Introgression-atlas link

?sample=<key or name> on the introgression atlas fills the Sample search and shows that sample (hook /*urlsample*/, hop_atlas/tools/patch_url_sample.py, deployed through atlas_deploy.py stage/deploy on 2026-10-10). Assembly haplotypes link to the row of their source plant where one exists. Not linked: SW75, one Wye RNA library (132_82F), drHumLupu and the MN1421/MN586 haplotypes.

Gaps