I myself have not tried using any of these tools, but this type of analysis is in my TODO list. I found this a couple of days ago and it looks very promising:
From their website:
Sibelia: A comparative genomics tool: It assists biologists in analysing 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: (1) shared regions, (2) regions that present in one group of genomes but not in others, (3) rearrangements that transform one genome to other genomes.
In version 2, Sibelia works with multiple strains of bacteria and partitions their genomes into synteny blocks — blocks of highly conserved regions among all compared genomes. It represents genomes in circos pictures [for publication] or interactive forms [for experts’ analysis].
Sibelia is under active development. If you see that Sibelia has a potential to support your research, please do not hesitate to contact us at firstname.lastname@example.org with a list of features you would like Sibelia to have.