The Users's manual is a good place to start if you need
information on various options. You can also click on 
to get help specific to that context.
The Tutorial is a good place to start if you would prefer to see an example worked through the AliWABA tools.
To cite this website, you can use the following reference:
AliWABA: Alignment on the Web with an A-Bruijn Approach
Neil Jones, Degui Zhi, and Ben Raphael
Submitted (BibTeX)
A Novel Method for Multiple Alignment of Sequences with Repeated and Shuffled Elements.
Benjamin Raphael, Degui Zhi, Haixu Tang, and Pavel Pevzner.
Genome Research (2004) 14,(11)2336-46. (BibTeX)
Identifying Repeat Domains in Large Genomes.
Degui Zhi, Benjamin Raphael, Alkes Price, Haixu Tang, and Pavel Pevzner.
Genome Biology 2006 7,(1):R7. (BibTeX)