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. 

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

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