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)