I would like to measure the similarity among set of operons from different species. Is there a well-known method for this? If you can suggest me some good articles addressing this problem, I will be thankful to you.
Hi, please try [GeneGrouper][1]

It will look for all gene clusters in a set of genomes that contain a gene of interest. It will then show how similar those gene clusters are between taxa. 


  [1]: https://github.com/agmcfarland/GeneGrouper