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Disclaimer:

This software is under development and provided as-is. We cannot guarantee that it is free of bugs,
nor has it been tested on all systems.
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* hbase-genomes module provides all utilities for uploading genomes, generating and indexing references, and alignment if desired.
* figg module creates small (<1kb) mutations, see http://www.biomedcentral.com/1471-2105/15/149
* kiss-population provides the optimization code for selecting cytogenetic bands to combine. This is incorporated into hbase-genomes 'gasearch' but can be used as a stand-alone by a script. This module does not require Hadoop.
* derby-db and kiss-derby are not recommended for use. These create the derby databases used by figg and kiss, but are not prepared for separate packaging.

At this time the software is developed to use HBase and Hadoop Map/Reduce. See http://insilicogenome.sourceforge.net for instructions.