Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages.

Abstract

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. Source code and manual are freely available in https://github.com/AADavin/ZOMBI/. Supplementary data are available at Bioinformatics online.