Recommended method for finding operons?

This could be great for identifying operons. Do you have any examples of using this tool to identify common operons? For example, nif operons or others involved in nitrogen fixation.

Yeah, exactly, that's a great use case. I have used Pynteny before to search for the Nif operon, also helping to tell paralogs apart from homologs.

I created a small case study to illustrate how this works.