Jalview is a free cross-platform program for multiple sequence alignment editing, visualisation and analysis. Use it to align, 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, and provides a linked view of aligned DNA and Protein products. It uses Jmol to view 3D structures, and VARNA to display RNA secondary structure, and can also use Chimera, ChimeraX and Pymol for 3D structure visualisation.

Experimental and predicted (eg alphafold and swiss-model) 3D structures for proteins can be automatically discovered via the 3D-Beacons network, and sequences and alignments retrieved from databases hosted at EMBL-EBI. The Jalview Desktop also 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 about the Jalview project. 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. The web based JalviewJS app is available via the JalviewJS link. The web based version 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).

Availability

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

ELIXIR-UK Resource

Jalview is a member of ELIXIR - the European-wide project providing high quality and sustainable infrastructure for biological information. Jalview was one of the first round of UK projects to be recognised as a “Tier 1” resource by ELIXIR-UK for Protein Structure and Function.