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Journal Publications
If you use Jalview in your work, please cite the Jalview 2 publication:
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Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M., Barton, G.J (2009),
"Jalview version 2: A Multiple Sequence Alignment and Analysis Workbench," Bioinformatics doi: 10.1093/bioinformatics/btp033
- Clamp, M., Cuff, J., Searle,
S. M. and Barton, G. J. (2004),
"The Jalview Java Alignment Editor," Bioinformatics, 20, 426-7
Program Documentation
Jalview 2+ Documentation
The Jalview Desktop application has an integrated searchable help system. The pages here
are the static HTML pages which make up the help system.
How do I edit sequences in
Jalview?
A quick guide to mouse and keystroke alignment editing in Jalview 2.
The Jalview 2.7 Manual (5MB Screen Optimized or 40MB 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).
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