I need to do some staff on genome alignment of a few bacterial genomes to detect some conserved genes with synteny among them. However, since some of them have diverged for a long time (probably up to about 1 billion years), many software that are available may not work properly (mainly designed for plant and vertebrate genomes). Is there any suggestion? Thanks in advance!
To what end? In my experience, genome alignments only work with closely related species.
+1, I agree that there needs to be a purpose. You're right in that alignments need homologous regions, but I would argue that most bacteria have some homologous regions that may be aligned. This still does not make genome alignment a valuable or meaningful exercise unless a research focus or question is present.