From Nikolay Vyahhi:
Sibelia is a fast synteny blocks generation tool for many closely related microbial genomes. It assists biologists in analyzing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments. Sibelia will also be helpful for the evolutionary and genome rearrangement studies for multiple strains of microorganisms. Sibelia is useful in finding shared regions, regions that present in one group of genomes but not in others, and rearrangements that transform one genome to other genomes.