Best way to search for alignments across whole genomes?

[kevbonham]

I have 10 bacterial genomes that my lab sequenced from a single environment, and I'd like to look for evidence of horizontal gene transfer between species within the environment.

So what I'd like to do is compare the genomes we have and look for regions of high (say >99% identity) similarity within a genome that has an overall identity that's significantly lower.

I suspect this is fairly easy, but there are a crap ton of tools and I don't have a sense of what the best way to go about this would be. I've got either raw, assembled, or annotated sequences - does it matter which of these I start with?

[GenoMax]

Mauve is a great tool for comparing genomes.