ActionMap: a web-based software that automates loci assignments to framework maps. - Guillaume Albini; Matthieu Falque; Johann Joets (Nucleic Acids Res., 2003)

BioMercator: integrating genetic maps and QTL towards discovery of candidate genes. - Anne Arcade; Aymeric Labourdette; Matthieu Falque; Brigitte Mangin; Fabien Chardon; Alain Charcosset; Johann Joets (Bioinform., 2004)

IRILmap: linkage map distance correction for intermated recombinant inbred lines/advanced recombinant inbred strains. - Matthieu Falque (Bioinform., 2005)

CODA (CrossOver Distribution Analyzer): quantitative characterization of crossover position patterns along chromosomes. - Franck Gauthier; Olivier C. Martin; Matthieu Falque (BMC Bioinform., 2011)

SeSAM: software for automatic construction of order-robust linkage maps. - Adrien Vidal; Franck Gauthier; Willy Rodrigez; Nadège Guiglielmoni; Damien Leroux; Nicolas Chevrolier; Sylvain Jasson; Elise Tourrette; Olivier C. Martin; Matthieu Falque (BMC Bioinform., 2022)