From Amy Sprenkle:
"We from cohort 11 adopted a Cluster J phage in the spring of 2019 to make sure we really got trained in all of the bioinformatics tools available. Hannaconda did not disappoint. I relied heavily on the Pope J Cluster paper for guidance, and worked on the TAC frameshift successfully from the excellent bioinformatics guide and help from Welkin. We used PECAAN and had two tRNAs called, and I learned at the symposium that the web-based aragorn would call introns as well. I failed to throughly explore this tool before submitting the genome, so I will continue to work on that. I message in this string because when searching for J cluster and introns, this is what pops up. It is not at all clear to me how one uses phamerator to see the introns, because they are not described in phamerator the way they are in the paper. Also, some of the J phage from the paper have an intron and others do not. Those that do are not consistent with regard to their association with HNH endonucleases.
Any help with better calling of an intron would be appreciated."