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.
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.
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