Geno-Diver: A combined coalescence and forward-in-time simulator for populations undergoing selection for complex traits

Geno-Diver is a combined coalescence and forward-in-time simulator designed to simulate complex traits with a quantitative and/or fitness component and implement multiple selection and mating strategies utilizing pedigree or genomic information. The simulation is carried out in two steps. The first step generates whole-genome sequence data for founder individuals. A variety of trait architectures can be gener- ated for quantitative and fitness traits along with their covariance. The second step generates new individuals forward-in-time based on a variety of selection and mat- ing scenarios. Genetic values are predicted for individuals utilizing pedigree or genomic information. Relationship matrices and their associated inverses are gener- ated using computationally efficient routines. We benchmarked Geno-Diver with a previous simulation program and described how to simulate a traditional quantita- tive trait along with a quantitative and fitness trait. A user manual with examples, source code in C++11 and executable versions of Geno-Diver for Linux are freely available at https://github.com/jeremyhoward/Geno-Diver.