# References

If you use this software, please cite:

- Néron, B.; Littner, E.; Haudiquet, M.; Perrin, A.; Cury, J.; Rocha, E.P.C. IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella. Microorganisms, 2022, 10, 700. https://doi.org/10.3390/microorganisms10040700

- Identification and analysis of integrons and cassette arrays in bacterial genomes Jean Cury; Thomas Jove; Marie Touchon; Bertrand Neron; Eduardo PC Rocha. Nucleic Acids Research, 2016; doi: 10.1093/nar/gkw319

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 the function –func_annot which uses NCBIfam-AMRFinder hmm profiles:

> - Haft, DH et al., Nucleic Acids Res. 2018 Jan 4;46(D1):D851-D860 PMID: 29112715