Sealion is a fast, interactive viewer for large multiple sequence alignments, designed for genomic epidemiology workflows. It can display annotated genome structure, colour sequences by nucleotide or amino acid scheme, highlight differences from a reference, and summarise variation with a per-column plot strip and an overview minimap.
Using Sealion
Web app
The easiest way to use Sealion is directly in your browser — no installation required:
https://artic-network.github.io/sealion
Drag and drop a FASTA file onto the viewer window, or use File → Open alignment. Load a GenBank (.gb) reference genome to display annotated CDS features, colour sequences relative to the reference, and navigate between sites that differ from it.
Desktop app
A native desktop application is available for macOS, Windows, and Linux, built with Tauri. It offers the same features as the web app with native file system access and the ability to open FASTA files directly from your file manager.
Pre-built installers for the latest release can be downloaded from the GitHub Releases page:
| Platform | Installer |
|---|---|
| macOS — Apple Silicon (M1/M2/M3/M4) | Sealion_x.x.x_aarch64.dmg |
| macOS — Intel (x86-64) | Sealion_x.x.x_x64.dmg |
| Windows | Sealion_x.x.x_x64-setup.exe |
| Linux (Debian/Ubuntu) | sealion_x.x.x_amd64.deb |
| Linux (AppImage) | sealion_x.x.x_amd64.AppImage |
Key features
- Colour schemes — several nucleotide and amino acid palettes; optionally highlight only sites that differ from the reference or consensus
- Plot strip — per-column conservation (entropy) or differences-from-reference bar chart
- Overview minimap — compressed whole-alignment view with genome structure, variable sites, and a sliding-window plot line
- Column collapse — compress uninformative regions to focus on variable sites
- Sort sequences — by name, tag, date, length, similarity to reference, or metadata from FASTA headers
- Tags & bookmarks — assign colour labels to sequences and mark columns for quick navigation
- Copy as FASTA — select a rectangular region and copy to the clipboard
Source code & issues
Sealion is open-source software. Source code and issue tracker are on GitHub: https://github.com/artic-network/sealion