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Here we present Zombi, a tool to simulate the evolution of species, genomes and sequences in silico, that considers for the first time the evolution of genomes in extinct lineages. ... It also incorporates various features that have not to date been combined in a single simulator, such as the possibility of generating species trees with a pre-defined variation of speciation and extinction ... Acknowledgements We thank Vincent Daubin, Wandrille Duchemin, Nicolas Lartillot and Thibault Latrille for insightful discussions during the preparation of this manuscript. ...doi:10.1093/bioinformatics/btz710 pmid:31566657 pmcid:PMC7031779 fatcat:wfyywcllkreblankienj7tiama