Jalview Manual

Screenshot of Jalview Manual cover

The manual is a comprehensive guide containing a range of practical exercises to help you explore the many functions available in Jalview.

Low-resolution PDF for on-screen viewing of the Jalview Manual

High-resolution PDF for printing of the Jalview Manual

Quick Guide

A quick guide to mouse and keystroke alignment editing in Jalview 2:

How do I edit sequences in Jalview?

Jalview Help

F1 overlaid on screenshoot

Pressing F1 in the Jalview Desktop will open the built-in help system, which can also be searched.

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)