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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.