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!
This question gets asked quite frequently around here -- see these answers for more information:
I would disagree with you that the software works preferentially for Eukaryotes over Bacteria or Archaea. I have used the same synteny tools on plants, fungi, and bacteria (some viruses too) with similar results. I would recommend Mauve and Symap for synteny anaysis, BRIG for bacterial synteny analysis and visualization, and Circos for visualization, but there are many other tools out there to choose from.