iPhy: an integrated phylogenetic workbench for supermatrix analyses. - Martin O. Jones; Georgios D. Koutsovoulos; Mark L. Blaxter (BMC Bioinform., 2011)

AvP: A software package for automatic phylogenetic detection of candidate horizontal gene transfers. - Georgios D. Koutsovoulos; Solène Granjeon Noriot; Marc Bailly-Bechet; Etienne G. J. Danchin; Corinne Rancurel (PLoS Comput. Biol., 2022)