Abstract
Summary 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 nonequilibrium 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/kernlab/discoal_multipop) under a GNU General Public License.
Contact kern{at}dls.rutgers.edu
Supplementary information Supplementary Figures and Text are appended below
