A simulation test bed for hypotheses of genome evolution

Motivation: Microbial genomes undergo evolutionary processes such as gene family expansion and contraction, variable rates and patterns of sequence substitution and lateral genetic transfer. Simulation tools are essential for both the generation of data under different evolutionary models and the validation of analytical methods on such data. However, meaningful investigation of phenomena such as lateral genetic transfer requires the simultaneous consideration of many underlying evolutionary processes. Results: We have developed EvolSimulator, a software package that combines non-stationary sequence and gene family evolution together with models of lateral genetic transfer, within a customizable birth-death model of speciation and extinction. Here, we examine simulated data sets generated with EvolSimulator using existing statistical techniques from the evolutionary literature, showing in detail each component of the simulation strategy.