Jalview is a free program for multiple sequence alignment editing, visualisation and analysis. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation.

Jalview description diagram

Jalview has built in DNA, RNA and protein sequence and structure visualisation and analysis capabilities. It uses Jmol to view 3D structures, and VARNA to display RNA secondary structure. The Jalview Desktop can also connect with databases and analysis services, and provides a graphical interface to the alignment and analysis services provided by the JavA Bioinformatics Analysis Web Services framework.

Finding out more

The About section provides more information. The Jalview Desktop App installs on most operating systems, and is available via the Download page, along with links to compiled jars and source code. An alpha release of the web based JalviewJS app is also available via the JalviewJS link. The web based version of Jalview is the same Jalview Java program, but compiled into JavaScript with Java2Script and SwingJS (with thanks to Bob Hanson of St Olaf’s College, USA).


Jalview is an open source project released under the GPL. Its development is coordinated by Jim Procter and Geoff Barton in the Computational Biology group at the University of Dundee, School of Life Sciences with support from the Biotechnology and Biological Science Research Council and the Wellcome Trust.

ELIXIR-UK Resource

Jalview is a proud member of ELIXIR - the European-wide project providing high quality and sustainable infrastructure for biological information. Following a strict selection procedure, Jalview has been identified as a “Tier 1” resource by ELIXIR-UK (Protein Structure and Function).