PrimAeon: selection analysis in seconds, in your browser

The HyphAeon team

PrimAeon is live: you can now paste a codon alignment into a browser tab and watch a selection report stream back in seconds. No account, no install, no upload — the inference runs entirely on your device.

Why this is fast enough to matter

PrimAeon is powered by HyphAeon, a phylogenetic foundation model that acts as a neural surrogate for HyPhy's likelihood methods. The headline number from the preprint is speed: site-level episodic selection inference comparable to MEME at 100×–1,100× the speed of maximum-likelihood estimation. Analyses that used to justify a coffee break — or a cluster job — now finish before the page has finished scrolling.

That speed changes what the analysis is for. A selection scan stops being a deliberate, budgeted step and becomes something you can do speculatively: screen every gene in an alignment set, sanity-check a hypothesis before committing to a full study, or triage an outbreak sequence the moment it arrives.

What you get

One alignment in, one report out:

  • Site-level selection — the neural MEME surrogate
  • Co-selection networks — which sites evolve together
  • Digital deep mutational scanning — predicted effect of every substitution
  • Phenotype association — sites linked to a trait you describe (a curated preset, a foreground list, or a table)

Because these results are generated by a neural surrogate model, every report is flagged is_surrogate and includes a direct path to verify the findings using exact maximum-likelihood methods on Datamonkey.

A tree is optional. Supply one with branch lengths and it is used as given; without one, PrimAeon works tree-free from pairwise TN93 distances.

Private by construction

Because the models ship as ONNX graphs running on ONNX Runtime's WebAssembly backend — the analysis pipeline itself ported to JavaScript — your sequences never leave the browser tab. For sensitive data — pre-publication genomes, clinical cohorts, surveillance data under embargo — that removes the upload question entirely rather than merely answering it.

The other half: ChronAeon

The same foundation model powers ChronAeon, the "radar" to HyphAeon's "microscope": molecular clock dating, R₀/Rₜ phylodynamics, phylogeography, and streaming genomic triage — analyses that reproduce landmark benchmarks (the 1931 HIV-1 group M origin date, H5N1 dispersal routes, 2009 H1N1 growth rates) in seconds rather than MCMC hours. ChronAeon is Python today (pip install chronaeon); see the docs. PrimAeon itself also has a dated route — /time fits a molecular clock and runs temporal selection in the browser, BEAST XML included.

HyphAeon is also wrapped for Galaxy — installed on usegalaxy.eu, with ChronAeon wrappers in progress — useful when you want web-based batch runs, or to customize an analysis beyond what PrimAeon's one-report interface offers.

Try it, then dig in

HyphAeon is supported in part by BRC Analytics and the NIH/NIAID.