Sealion is a fast, interactive viewer for large multiple sequence alignments, built for genomic epidemiology workflows. It runs entirely in the browser as a webapp and is also available as a native desktop application for macOS, Windows, and Linux.
The easiest way to use Sealion is directly in your browser — no installation required.
Open the webapp: https://artic-network.github.io/sealion
Drag and drop a FASTA file onto the viewer window, or use File → Open alignment. Sealion accepts:
- FASTA (
.fasta,.fa,.fna,.ffn,.faa,.frn)
Click Load reference (the green button) to load a GenBank (.gb) or JSON reference genome file. Once loaded, Sealion can:
- Display annotated CDS features in the overview minimap
- Colour sequences relative to the reference
- Navigate between sites that differ from the reference
| Region | Description |
|---|---|
| Toolbar | Controls for font size, colour scheme, column collapse/expand, colouring, plot type, overview layers, sort, search, tags, and bookmarks |
| Labels panel | Sequence names; click to select, drag to reorder |
| Alignment canvas | Main sequence view with scrolling and zooming |
| Header | Column positions and consensus sequence |
| Overview minimap | Compressed view of the whole alignment with genome structure, variable sites, and a sliding-window plot |
| Plot strip | Per-column entropy or differences-from-reference bar chart |
Use the Colour menu to choose from several nucleotide or amino acid colour schemes. Select Colour differences only to highlight only sites that differ from the reference or consensus — identical sites fade to grey.
The Plot menu switches between:
- Conservation (entropy) — high bar = conserved site (Fire colour palette)
- Differences from reference — high bar = many sequences differ (Ocean colour palette)
- Hide plot / Show plot — toggle the strip on/off
The Overview menu toggles individual layers of the minimap:
- Genome structure — CDS feature bars colour-coded by reading frame (click a CDS to select those columns; double-click to zoom)
- Compressed sites — tick marks for masked/collapsed columns
- Variable sites — tick marks at each polymorphic site, coloured by the consensus nucleotide/amino acid
- Plot line — sliding-window average of the active plot, scaled to fill the height
Select columns and press Collapse (or Ctrl/⌘ −) to compress uninformative regions. Collapsed columns are shown as narrow markers. Toggle their visibility with Ctrl/⌘ H.
The Sort menu sorts sequences by name, tag, date, length, similarity to reference, or other metadata fields parsed from FASTA headers.
- Tags — assign colour labels to selected sequences via the Tags menu
- Bookmarks — mark specific alignment columns for quick reference via the Bookmark menu
- Click and drag on the alignment to select a rectangular region
Ctrl/⌘ Ato select all columnsCtrl/⌘ Cto copy selected sequences as FASTA to the clipboardShift+Ctrl/⌘ Cto copy sequence names only
| Action | macOS | Windows / Linux |
|---|---|---|
| Navigate | ← → ↑ ↓ | ← → ↑ ↓ |
| Page scroll | ⌥ + ← → ↑ ↓ | Alt + ← → ↑ ↓ |
| Jump to edges | ⇧ + ← → ↑ ↓ | Shift + ← → ↑ ↓ |
| Next/prev difference | ⌘ > / ⌘ < | Ctrl > / Ctrl < |
| Colour differences only | ⌘ D | Ctrl D |
| Toggle hide mode | ⌘ H | Ctrl H |
| Collapse columns | ⌘ − | Ctrl − |
| Expand columns | ⌘ = | Ctrl = |
| Reset / change font size | ⌘ 0 / ⌥⌘ ± | Ctrl 0 / Alt+Ctrl ± |
| Select all columns | ⌘ A | Ctrl A |
| Copy as FASTA | ⌘ C | Ctrl C |
| Copy labels | ⇧⌘ C | Shift+Ctrl C |
| Move sequences up/down | ⌘ ↑ / ⌘ ↓ | Ctrl ↑ / Ctrl ↓ |
| Drag sequences | ⌥⌘ + drag label | Alt+Ctrl + drag label |
| Search next / prev | ⌘ G / ⇧ Enter | Ctrl G / Shift Enter |
| Pan view | Space + drag | Space + drag |
The Sealion desktop app is built with Tauri and provides native performance with direct file system access.
Pre-built installers for the latest release are available on the GitHub Releases page.
| Platform | File |
|---|---|
| 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 |
If you are unsure which Mac build to use: click the Apple menu → About This Mac. If the Chip line reads Apple M… download the Apple Silicon build; if it reads Intel download the Intel build.
- Download the
.dmgfor your Mac's processor (see above). - Open the
.dmgand drag Sealion.app into your Applications folder. - Launch Sealion from Applications. The app is code-signed and notarised by Apple, so macOS will open it without any security warnings.
FASTA files can be opened by double-clicking them in Finder once Sealion is installed.
- Download the
.exeinstaller from the Releases page. - Run the installer and follow the prompts.
- Windows SmartScreen may display a warning for unsigned executables. Click More info → Run anyway.
Debian/Ubuntu (.deb):
sudo dpkg -i sealion_x.x.x_amd64.debAppImage:
chmod +x sealion_x.x.x_amd64.AppImage
./sealion_x.x.x_amd64.AppImageRequirements: Rust (stable) and Node.js (≥ 18).
# Clone the repository
git clone https://github.com/artic-network/sealion.git
cd sealion
# Install JavaScript dependencies
npm install
# Run in development mode (opens a native window)
npm run dev
# Build a release installer for the current platform
npm run buildBuilt installers are placed in src-tauri/target/release/bundle/.
Sealion was designed and developed by Andrew Rambaut at the University of Edinburgh as part of the ARTIC Network project.
- Source code: github.com/artic-network/sealion
- Issues & feature requests: github.com/artic-network/sealion/issues
- ARTIC Network: artic.network
Sealion is open-source software. See LICENSE for details.