Jalview is free to end-users because of support from the UK's BBSRC and The Wellcome Trust

If you would like to see Jalview continue to be available then please take a few minutes to write us a support letter saying how you use Jalview in your research/teaching.

Write as a PDF including your institution's heading and send to:
support_jalview@bartongroup.org by Friday 19th October 2018.

Thank you all those who have already written such nice letters!

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)