Aligning many long sequences 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)
Whole genome aliment can be done using Progressive Mauve, LAST or Mummer. For bacteria I used Mauve since it has also very nice visualisation engine. A very new tool is Minimap2, a super fast mapper that supposed beside read mapping be able to handle reference vs reference. However, I do not know how performance of it compares to the tools mentioned above.

If you are interested in a rough idea of the shared genome regions, you can use bevel. Bevel is not really an aligner, it is more like a dot-plot, but it is super fast (even for mammalian sized genomes).