Jalview is a free program for multiple sequence alignment editing, visualisation and analysis

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.

• JalviewLite is the web based version of Jalview, and used on many web sites (there's a list here)
• The Jalview Desktop is for biologists and bioinformaticians who need to create, curate, analyse and publish multiple sequence alignments.

Jalview has built in DNA, RNA and protein sequence and structure visualisation and analysis capabilities, and 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, and the links at the top of the page will let you launch the Jalview Desktop, try out the JalviewLite applet demonstration pages. The Download page lets you get a Jalview Desktop installer for your system, and links to compiled jars and source code.

Availability

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's College of Life Sciences with support from the UK's Biotechnology and Biological Science Research Council.