I am looking for comparative genomics tools for comparing two or more bacterial genomes
COG may be a good option. https://academic.oup.com/nar/article/49/D1/D274/5964069
There are many of them: Roary, proteinortho, ppanggolin, panaroo, get_homologues... All these tools works in a command-line environment, but you can find others, with more limitations, for windows or online environments, such as orthovenn and others
Thank You Zaki Saati Santamaria. I found orthovenn2 as very good one and user friendly. But works with proteins. May I Know, if similar platforms for DNA are available as well?
I don't think there is a tool out there that will do much more than the ones listed in the answers you have already received.
Unless the bacteria are very closely related, it generally doesn't help to compare them at the DNA level. The vast majority of bacterial DNA codes for protein, so the comparison is more sensitive at the protein level. Protein-coding genes in bacteria are generally organized into operons, groups of related proteins which are transcribed together to make a single mRNA which is then translated, potentially from different starting points, to create each individual protein it encodes. Most bacterial comparison tools also have information about whether two proteins are in the same operon, so this too can be compared. Finally, higher-level organization of operons along a bacterial chromosome is not highly conserved, even closely related species within the same genus will sometimes differ markedly at this level. There is very little information to be gained from comparisons at this level, so tools generally don't support such comparisons. If your species are closely enough related to share synteny beyond the operon level, though, dot-plot comparisons are the tools to look for.
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