If you use Jalview in your work, please cite the Jalview 2 publication:

• Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M., Barton, G.J (2009),
  "Jalview version 2: A Multiple Sequence Alignment and Analysis Workbench,"
  Bioinformatics doi: 10.1093/bioinformatics/btp033
  
  
• Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004),
  "The Jalview Java Alignment Editor," Bioinformatics, 20, 426-7

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

How do I edit sequences in Jalview?
A quick guide to mouse and keystroke alignment editing in Jalview 2.

The Jalview 2.7 Manual (5MB Screen Optimized or 40MB Print Version)
This is a comprehensive user manual with exercises, written by David Martin, Jim Procter, Geoff Barton and Andrew Waterhouse.

Old documentation preserved for posterity 

Jalview Quickstart Guide
A quick reference for Jalview 2.0 that was produced for its first release in 2005.

Jalview 1.18 Documentation
The original help documentation for Jalview version 1 (published in Clamp et. al 2004).