FASTGA v1.0

Initial release of FastGA, a very rapid genome comparator that finds alignments between two genomes or within a single genome. It is very sensitive, finding all alignments over 100bp at 70% or greater identity, except potentially in very repetitive regions. Alignments do not contain large gaps (> 40bp or so) - the philosophy is to handle these by chaining series of alignments in a postprocessing step. We consider FastGA to be the first step in whole genome alignment which is to find the subset of the reported alignments that are homologous due to evolution.