I'm faced with having to align many (some 100s) bacterial genomes, where the genome length is in the millions. Obviously, this is beyond normal alignment techniques and it's unclear to me what the best practice is for such circumstances:
- conventional alignment on a very powerful computer with lots of memory
- break up the genome into smaller fragments and align them individually
- some exotic different procedure
What possible avenues of attack are there?
(I've attempted to use Mafft and Clustal with little success)