v0.1.0-alpha.14

Decoding-Us Navigator — v0.1.0-alpha.14 (prerelease)

✨ Neanderthal ancestry

Everyone whose ancestry is partly outside Africa carries a little Neanderthal DNA, from interbreeding roughly 50,000 years ago. Navigator now measures yours — in Ancestry for the full picture, and in plain language in Simple mode.

• A count, not a percentage. You get the number of archaic marker copies you carry, out of the number your test could actually check, split into Neanderthal-diagnostic and shared-archaic — plus how that ranks against reference samples of similar ancestry ("more than X% of European samples"). It is deliberately not phrased as "you are N% Neanderthal". The measurement doesn't support that claim.
• Not comparable to another company's number. Every test counts against its own marker panel and its own denominator, so two "Neanderthal variant" counts are not the same measurement even when they use the same words. Navigator's panel holds 299,958 sites.
• No Denisovan result. Outside Oceania that signal sits at the noise floor, so printing one would be inventing a finding. The app says nothing rather than something confident and wrong.
• Where it sits on your chromosomes. A separate Archaic segments card locates the introgressed tracts themselves and draws them per chromosome. Whole-genome data only, and it needs de-novo variant calling to have been run first — that pass takes hours, so the card asks you to run it rather than starting one behind a button click and looking like it has hung.
• Ask what it means. The per-signal Explain this button covers the archaic result, and the results chat and HTML export both carry it.

How much does it find? — measured against a published callset

The segment caller was calibrated and then checked against hmmix's own 1000 Genomes archaic calls, not against a target we picked. On the ground-truth European genome:

Archaic sequence located	91.5 Mb across 2,084 tracts
Share of the callable genome	5.04%
Published European average (hmmix, n=633)	90.9 Mb (p10 84.6 – p90 97.2)

That lands at 1.01× the published mean, comfortably inside the normal range — on one genome. That is a calibration check, not a validation across people.

What is deliberately withheld. The machinery to label each tract Neanderthal or Denisovan is built, tested, and switched off. On this genome the two lineages' signals differ by a ratio of 1.10 — barely distinguishable — and forcing a call produced 0 Mb Neanderthal against 0.48 Mb Denisovan, the exact inverse of the known pattern for a European. Shipping that would have manufactured a Denisovan finding out of noise. Segments are shown simply as archaic, and the card says so.

✨ Simple mode, rebuilt around a section rail

Simple mode is what new users land in, and it had become a single scroll several screens tall — ancestry, ancient ancestry, Neanderthal markers, shared ancestry, chromosome painting, relatives and the chat all stacked in one column. Nothing in it was findable.

• Six panels behind a rail: Your story · Paternal line · Maternal line · Ancestry · Relatives · Your test. The rail carries each panel's headline value — your terminal haplogroup, your top ancestry, your match count — so it answers most questions before you click anything.
• Ancestry now reads forwards in time. Deep origins (ancient source populations) → Neanderthal traces → continent → detailed populations → your two parental sides → shared ancestry. Top to bottom is oldest to most recent.
• Relatives are grouped by closeness — close family, extended family, distant relatives — and every row states what its grouping is based on: measured shared DNA where you've actually exchanged segments with someone, or an estimate from shared signals where you haven't. Those are very different claims and the list no longer blurs them.
• The AI story replaces the one-line summary instead of sitting on top of it, with the plain version one click away.

Also new

• Settings is split into sub-tabs — General, Connection, Ancestry, AI, References, Tools, Advanced — instead of one long dialog.
• Pick your reference genome during first-run setup, so a first import doesn't have to guess or stall on a multi-gigabyte download you didn't choose.

Fixed

• The Simple-mode subject list took half the window. All five left panels shared one saved width, so the wide Advanced subjects table dictated how much room a plain list of names got. Each now remembers its own.
• Missing-glyph boxes in the navigation. Several icons — including the one on "My DNA" — had no glyph in the app's font and rendered as empty squares. Replaced, and there's now a test that fails if anyone adds another.

Under the hood

• The download is bigger this time — roughly 60 MB more than alpha.13. Five new reference assets back the archaic report (the marker panel, the percentile reference, an African-outgroup track, diagnostic-site classification, and a callability mask), and they currently ship inside the installer rather than downloading on first use. Trimming that back is on the list.
• New CLI subcommand navigator archaic-segments.
• A simplification pass over the app and UI: the largest files split by domain, duplicated logic given one home, and per-frame view caches added.

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Prerelease build. Installers below: macOS .dmg (universal), Windows -setup.exe, Linux .AppImage / .deb. Verify against SHA256SUMS.

Full changelog: v0.1.0-alpha.13...v0.1.0-alpha.14