Looking for the 'Launch Jalview' buttons ?

You need to download an installer to run Jalview 2.11.
You can still use webstart to access old versions of Jalview in the version archive

Jalview Help
 
Pressing F1 in the Jalview Desktop will open the built-in help system, which can also be searched
F1 in JalviewLite will open the help pages in your browser
How do I edit sequences in Jalview? A quick guide to mouse and keystroke alignment editing in Jalview 2
The Jalview Manual
Low-resolution for on screen
High-resolution 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)