AcCNET (Accessory Genome Constellation Network): comparative genomics software for accessory genome analysis using bipartite networks. - Val F. Lanza; Fernando Baquero; Fernando de la Cruz; Teresa M. Coque (Bioinform., 2017)

PLACNETw: a web-based tool for plasmid reconstruction from bacterial genomes. - Luis Vielva; María de Toro; Val F. Lanza; Fernando de la Cruz (Bioinform., 2017)

PATO: Pangenome Analysis Toolkit. - Miguel D. Fernández-de-Bobadilla; Alba Talavera-Rodríguez; Lucía Chacón; Fernando Baquero; Teresa M. Coque; Val F. Lanza (Bioinform., 2021)