References

If you use this software, please cite:

• Cury J, Jové T, Touchon M, Néron B, Rocha E.P.C. (2015) Automatic and accurate identification of integrons and cassette arrays in bacterial genomes reveals unexpected patterns, bioRxiv doi: http://dx.doi.org/10.1101/030866

Please cite also the following articles:

• Nawrocki, E.P. and Eddy, S.R. (2013) Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics, 29, 2933-2935.
• Eddy, S.R. (2011) Accelerated Profile HMM Searches. PLoS Comput Biol, 7, e1002195.
• Hyatt, D., Chen, G.L., Locascio, P.F., Land, M.L., Larimer, F.W. and Hauser, L.J. (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics, 11, 119.

and if you use functional annotation, cite the corresponding articles:

• Gibson, M.K., Forsberg, K.J. and Dantas, G. (2015) Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology. ISME J, 9, 207-216.