RecPhyloXML: a format for reconciled gene trees. - Wandrille Duchemin; Guillaume Gence; Anne-Muriel Arigon Chifolleau; Lars Arvestad; Mukul S. Bansal; Vincent Berry; Bastien Boussau; François Chevenet; Nicolas Comte; Adrián A. Davín; Christophe Dessimoz; David Dylus; et al. (Bioinform., 2018)

Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages. - Adrián A. Davín; Théo Tricou; Eric Tannier; Damien M. de Vienne; Gergely J. Szöllosi (Bioinform., 2020)