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

 

Current Jalview Manual

The manual is a comprehensive guide containing a range of practical exercises to help users explore the many functions available in Jalview. It's authors are David Martin, James Procter, Andrew Waterhouse, Saif Shehata, Nancy Giang, Mungo Carstairs, Charles Ofoegbu, Kira Mourão, Suzanne Duce and Geoff Barton.

  of the Jalview Manual
  of the Jalview Manual

 

Quick Guide

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

 

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)