Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004),
"The Jalview Java Alignment Editor," Bioinformatics, 20, 426-7
If you use Jalview in your work, please quote this publication.

How do I edit sequences in Jalview?

Jalview Quickstart Guide
A useful quick guide to the new look Jalview.

Jalview 2+ Documentation
Jalview 2+ has an integrated searchable help system. The pages here are the static HTML pages which make up the help system.

Jalview 1.18 Documentation
The original help documentation for Jalview.