snp-distsx

Browser-based pairwise SNP distance matrix calculator from aligned FASTA files.

snp-distsx is a web application implementing the snp-dists algorithm by Torsten Seemann (Melbourne Bioinformatics, University of Melbourne), reimplemented in TypeScript for the browser. No data ever leaves your machine.

Features

• Upload a multiple sequence alignment (FASTA or gzipped FASTA)
• Compute pairwise SNP distances entirely client-side — zero server uploads
• Interactive heatmap with colour-coded distance matrix (canvas-rendered)
• Distribution histogram with adjustable cluster threshold line
• Scrollable distance table with conditional cell formatting
• Export to TSV, CSV, or long/molten format
• Supports all snp-dists options: -a (count all), -k (preserve case), -c (CSV), -b (blank corner), -m (molten), -t (headers), -L (lower triangle), -x (max distance)
• Light/dark theme

Algorithm

Faithful TypeScript reimplementation of snp-dists v1.2.0 (Torsten Seemann, GPLv3).

For each pair of aligned sequences A and B, at each position i:

• Count a SNP if A[i] ≠ B[i] and neither A[i] nor B[i] is an ignore character
• By default, non-ACGT bases (gaps -, Ns, IUPAC ambiguity codes) are replaced with . and skipped
• Enable Count all differences (-a) to include these positions

Sequences are stored as Uint8Array (char codes) for fast inner-loop comparison.

Typical Workflow

snippy (per sample) → snippy-core → core.full.aln
                                          ↓
                    [optional] Gubbins → filtered_polymorphic_sites.fasta
                                          ↓
                              snp-distsx → interactive matrix + heatmap
                                          ↓
                            Export TSV/CSV for downstream analysis or phylogenetics

Input

A FASTA file where all sequences are the same length (a multiple sequence alignment or pseudo-alignment). Accepts .fasta, .fa, .fna, .aln, .fsa and .gz compressed variants.

Development

npm install
npm run dev       # start dev server at http://localhost:5173
npm run test      # run unit tests
npm run build     # production build to dist/
npm run check     # tests + lint + build (CI equivalent)

Docker

# Build image
docker build -t snp-distsx .

# Run (serves on http://localhost:8080)
docker run -p 8080:80 snp-distsx

Tests

Unit tests cover:

Module	Tests
parseFasta	Multi-line sequences, empty input, mismatched lengths, name parsing
computeMatrix	SNP counting, gap skipping, maxDiff early exit, symmetry
formatOutput	TSV/CSV, blank corner, lower triangle, molten format

npm run test

Attribution

Original snp-dists tool: Seemann T (2018). snp-dists: Pairwise SNP distance matrix from a FASTA sequence alignment. https://github.com/tseemann/snp-dists — GPLv3

Web application: Nabil-Fareed Alikhan <nabil@happykhan.com> Centre for Genomic Pathogen Surveillance, University of Oxford https://www.happykhan.com

License

GPL-3.0-only — in keeping with the original snp-dists licence.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, version 3 only.