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Jalview is a free, open-source program for editing, visualising and analysing multiple sequence alignments. It is developed at the University of Dundee and distributed from jalview.org as a desktop application, with a browser version called JalviewJS. This page explains what it does, who maintains it, where its documentation lives and how to cite it. Facts below come from the Jalview website and were read on 2026-11-07.
What Jalview is
The Jalview home page describes it as a “free cross-platform program for multiple sequence alignment editing, visualisation and analysis”. Beyond alignments, it also handles phylogenetic trees, principal component analysis (PCA) plots, 3D structure views and sequence annotation. It is released under the GPL, so the source is open.
It comes in two forms. The Desktop App installs on most operating systems. JalviewJS is the browser-based version. The FAQ also documents a --headless flag for running Jalview on servers without a display.
Who runs it and what it covers
Development is coordinated by James Procter and Geoff Barton in the Division of Computational Biology, School of Life Sciences, University of Dundee. The site lists support from the Wellcome Trust and UKRI BBSRC, and describes Jalview as an ELIXIR-UK “Tier 1” resource and a 2023 ELIXIR Recommended Interoperability Resource. Those designations matter if a grant report or data management plan asks which community-endorsed tools you used.
Integrations listed on the home page:
- 3D structure display with Jmol, and RNA secondary structure with VARNA.
- Linking to external viewers: Chimera, ChimeraX and PyMOL.
- Structure discovery through the 3D-Beacons network.
- Retrieval of sequences and alignments from EMBL-EBI databases.
- A graphical interface to JABAWS web services.
Getting started
The download page offers desktop installers for macOS (Intel and Apple Silicon), Windows (x64) and Linux (x64 and aarch64), plus a generic Unix script and archive, an executable jar, an administrator install and build-from-source instructions. Check that page for the current version number. The FAQ says that since release 2.11.1.0 the Linux 64-bit Intel installer bundles a Java runtime, while other Linux builds need Java installed separately.
Steps drawn from the official FAQ and help pages:
- Download the installer for your operating system from the Download page on jalview.org.
- Open an alignment file with File → Input Alignment → From File.
- Press F1 to open the built-in help at any point.
- If sequence names show unwanted “/start-end” suffixes on output, untick that option under Tools → Preferences → Output.
- If Jalview must reach the network through a proxy, set it under Tools → Preferences → Connections.
- If something fails, the FAQ describes opening the Java Console from the Desktop menu to see diagnostic output.
Learning material on the Help page includes a “Getting Started” video playlist, hands-on exercises, the FAQ, the Jalview Manual (PDF) and the Jalview Discussion Forum. A short quick guide, “How do I edit sequences in Jalview?”, is linked from the documentation page.
Jalview forms and where each fits
| Form | What the site says |
|---|---|
| Desktop App | Installs on most operating systems; the main download. |
| JalviewJS | Browser version. |
| Headless mode | The --headless flag is documented in the FAQ for server use. |
Strengths and limits
Strengths stated by the project: it is free and open source; it runs across platforms; it combines alignment editing with trees, PCA, annotation and structure views in one program; and the FAQ states that files saved by earlier versions are intended to be readable by later ones, which helps long-running projects.
Limits documented in the FAQ: some non-Intel Linux builds need Java installed separately, and Windows releases before 2.11.5.0 could crash for usernames with non-ASCII characters. Jalview edits and visualises alignments; it can call alignment web services through JABAWS, but the program itself is described as an editor and analysis workbench.
Adjacent tasks on CASRAI
This page does not rank competing alignment tools, because it only describes what Jalview’s own pages state. For work that sits next to an alignment, see our guide to making a phylogenetic tree, the guide to ESMFold protein structure prediction and the guide to the Addgene plasmid repository. For software-sharing practice, see open source software and the FAIR4RS software citation principles.
How to cite Jalview
The Jalview site gives this reference for the program:
Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ (2009). Jalview Version 2 – a multiple sequence alignment editor and analysis workbench. Bioinformatics 25(9):1189–1191. doi:10.1093/bioinformatics/btp033
In methods sections, also record the exact Jalview version you used.
FAQ
Is Jalview free?
Yes. The home page describes it as free and released under the GPL as an open source project.
Who develops Jalview?
The University of Dundee School of Life Sciences, with development coordinated by James Procter and Geoff Barton.
Which operating systems does it run on?
The download page lists installers for macOS, Windows and Linux, plus generic Unix packages. JalviewJS runs in a browser.
Do I need to install Java?
Per the FAQ, the Linux 64-bit Intel installer has included a Java runtime since 2.11.1.0; other Linux builds need Java installed.
Where do I get help?
Press F1 in the program, read the Manual, watch the Getting Started videos, or ask on the Jalview Discussion Forum, all linked from jalview.org/help.
Sources
- Jalview home page, https://www.jalview.org/ (read 2026-11-07)
- Jalview Help, https://www.jalview.org/help/ (read 2026-11-07)
- Jalview Download, https://www.jalview.org/download/ (read 2026-11-07)
- Jalview FAQ, https://www.jalview.org/help/faq/ (read 2026-11-07)
- Jalview Documentation, https://www.jalview.org/help/documentation/ (read 2026-11-07)
