Abstract
Here we describe discoal, a coalescent simulator able to generate population samples that include selective sweeps in a feature-rich, flexible manner. discoal can perform simulations conditioning on the fixation of an allele due to drift or either hard or soft selective sweeps, even those occurring a large genetic distance away from the simulated locus. discoal can simulate sweeps with recurrent mutation to the adaptive allele, recombination, and gene conversion, under non-equilibrium demographic histories and without specifying an allele frequency trajectory in advance. Availability and Implementation: Availability and implementation: discoal is implemented in the C programming language. Source code is freely available on GitHub (https://github.com/kern-lab/discoal_multipop) under a GNU General Public License.
