| 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 |
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| 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)