Prophinder: a computational tool for prophage prediction in prokaryotic genomes. - Gipsi Lima-Mendez; Jacques van Helden; Ariane Toussaint; Raphaël Leplae (Bioinform., 2008)

NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways. - Sylvain Brohée; Karoline Faust; Gipsi Lima-Mendez; Olivier Sand; Rekin's Janky; Gilles Vanderstocken; Yves Deville; Jacques van Helden (Nucleic Acids Res., 2008)

ACLAME: A CLAssification of Mobile genetic Elements, update 2010. - Raphaël Leplae; Gipsi Lima-Mendez; Ariane Toussaint (Nucleic Acids Res., 2010)