If you publish findings obtained using CheckAlign and wish to cite the tool, it is suggested that you use the following publication:

Muñoz-Pomer A, Futami R, Sempere JM, Moya A, Llorens C: CheckAlign 2.0 (2011). Biotechvana Bioinformatics: 2011-SOFT1.

If you also need to cite the Gypsy Database (GyDB) please use additionally the reference below of the last GyDB release:

Llorens, C., Futami, R., Covelli, L., Dominguez-Escriba, L., Viu, J.M., Tamarit, D., Aguilar-Rodriguez, J. Vicente-Ripolles, M., Fuster, G., Bernet, G.P., Maumus, F., Munoz-Pomer, A., Sempere, J.M., LaTorre, A., Moya, A. (2011) The Gypsy Database (GyDB) of Mobile Genetic Elements: Release 2.0 Nucleic Acids Research (NARESE) 39 (suppl 1): D70-D74 doi: 10.1093/nar/gkq1061