Welcome to Jalview's built in documentation.

If you don't know what Jalview is, then in addition to the pages here, we also suggest you take a look at www.jalview.org.

Here are some good places to start:

• What's New" summarises the new features in this release of Jalview.
• Learn how to edit alignments with Jalview.
• Import and display sequence features on your alignment
• Use Jmol to view and superpose 3D structures associated with sequences in the alignment

If you are using the Jalview Desktop application and are looking for something specific, then this help system also includes a search box. If you're already viewing this in your web browser, then google the online version of these pages. If you don't find what you are looking for, or want to report a bug or make a feature request, then get in contact over at http://www.jalview.org/community

Citing Jalview
If you use Jalview in your work, please cite the Jalview 2 paper in Bioinformatics:

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 25 (9) 1189-1191 doi: 10.1093/bioinformatics/btp033