What is Jalview?
Jalview is a multiple alignment editor written in Java. It is used widely in a variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain database) but is available as a general purpose alignment editor and analysis workbench.

If you're interested in learning how to use Jalview in depth, take a look at the documentation, or come to one of our Jalview training courses.

Jalview Development is supported from 2009 to 2014 by the BBSRC, and coordinated by Geoff Barton at the University of Dundee. Version 2 arose from the "VAMSAS" Project (BBSRC eScience 2004-2007), with consultancy (blessing :-) from Michele Clamp; the originator of Jalview.

Authors :
Version 2+ Andrew Waterhouse; Jim Procter; David Martin; Geoff Barton
Version 1+ Michele Clamp; James Cuff; Stephen Searle; Geoff Barton

Thanks to Andreas Prlic for code and suggestions for DAS feature capabilities and Benjamin Schuster-Böckler for his Stockholm parsing code, both from the Wellcome Trust Sanger Institute, Cambridge.

If you use Jalview in your work, please quote this publication:

Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
"Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
Bioinformatics 25 (9) 1189-1191 doi: 10.1093/bioinformatics/btp033