I've been interested in plasmid detection in bacterial genomes. I tried plasmidfinder and this software found only one plasmid in each of my two bacterial genomes. I was dubious about these results, because I read many genome announcements which found something like from 6 to 10 plasmids per genome around 5 -6 MB. I then used PlasmidSeeker and what I received in the result file was a list of 9 or 11 so called "plasmid clusters", each containing a few plasmids with complete ID. I know that my genome cannot contain tens of plasmids, so my question is which one(s) of them is (are) the real one(s)?
By the way, can you suggest other bioinformatics tools specially designed to detect plasmids in bacterial genomes?