SNP Site Extraction from Alignments — in your browser.
snp-sitesx is a privacy-first, client-side web tool that replicates the functionality of snp-sites by Sanger Pathogens. Extract SNP sites from multi-FASTA alignments with interactive visualisations — no data leaves your machine.
- VCF, Phylip, and SNP-FASTA export — same outputs as the snp-sites CLI
- SNP density and position visualisations — interactive Recharts plots
- Pairwise distance matrix — heatmap for up to 50 sequences
- Client-side — all computation happens in your browser
| CLI flag | Description |
|---|---|
-v |
Include VCF in export (default on) |
-p |
Include Phylip in export |
-m |
Include SNP-FASTA in export (default on) |
-r |
Include reference sequence in outputs |
-c |
Only ACGT columns (filter ambiguous) |
-b |
Include monomorphic sites |
npm install
npm run dev # Start dev server
npm run test # Run unit tests
npm run check # Type-check + lint + build- Vite + React 18 + TypeScript 5.6
- Recharts 2.x for visualisations
- Pure TypeScript SNP detection (no WASM)
- file-saver for downloads
GPL-3.0-only — see LICENSE