Zombi: A phylogenetic simulator of trees, genomes and sequences that accounts for dead lineages

Adrian A Davin (1) , Theo Tricou (1) , Eric Tannier (2) , Damien M. de Vienne (3) , Gergely J Szöllosi (4)

1 LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
2 BEAGLE - Artificial Evolution and Computational Biology
3 Le Cocon
4 BPGE - Bioinformatique, phylogénie et génomique évolutive

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 rates through time, simulating explicitly intergenic sequences of variable length and outputting gene tree - species tree reconciliations.

Domaines: Bio-informatique [q-bio.QM]

Adrian A Davin, Theo Tricou, Eric Tannier, Damien M. de Vienne, Gergely J Szöllosi. Zombi: A phylogenetic simulator of trees, genomes and sequences that accounts for dead lineages. Bioinformatics, 2019, ⟨10.1093/bioinformatics/btz710⟩. ⟨hal-02302010⟩