HYPHY-3 // SIMD128 WEBASSEMBLY WORKBENCH
Whole-Alignment Likelihood, Rooting & Unified Selection
Drop coding sequences (FASTA / NEXUS) to run reading-frame rescue, codon Pair-HMM + POA alignment, recombination routing, and joint codon/lineage selection forensics — 100% locally in your browser.
Drop Sequence File or Click to Browse
Unaligned or aligned
.fasta, .fa, .fna, .cds, .nex, or .json dossiers
100% Client-Side • Zero Data Leaves Your Machine
Pre-Loaded Benchmark & Diagnostic Cohorts
0 QA & Admission → 1 Codon POA → 2 Phylogeny & Recombination → 3 Unified Selection How it works →
Suggested Genetic Code:
Evaluating coding sequences…
Genetic Code
Minimum Length
15 codons
Minimum Homology Z-Score
Z ≥ 3.5
Pre-aligned input handling:
Admitted
—
Ready for alignment
Auto-Rescued
—
Frame / UTR adjusted
Quarantined
—
Filtered out
Cohort Profile
—
Median length & identity
Aligning admitted sequences in codon space…
Indel Window Refinement (Inside-Outside EM)
Alignment Mode
Alignment Span
—
Codon columns
Gap-Free Core
—
In-frame conservation
Homology Confidence
—
Mean P_hom across columns
Indel & Frameshift QC
—
Repairs & indel windows
Optimizing codon phylogeny and scanning for recombination breakpoints…
Coupled SPR Topology Search
Localized Recombination & Reticulation Scan
Tree Length
—
subs/codon
Global ω (MG94)
—
Tree-wide dN/dS
Recombination
—
Breakpoint routing
GC3 Composition
—
3rd-position GC range
Click any node or branch to inspect statistics or tag a custom
{Foreground} clade
● Orange = Focal Clade • ● Slate = Background
Running unified evolutionary selection forensics…
Gene-Wide (BUSTED)
—
Episodic diversification test
Adaptive & PRIME Sites
0
MEME • FEL • Contrast • PRIME
Lineage Regimes
—
RELAX • aBSREL
Conserved & Epistasis
—
Purifying core & co-evolution