Andrew D Kern1,2, Daniel R Schrider2. 1. Department of Genetics. 2. Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08554, USA.
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 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: discoal is implemented in the C programming language. Source code is freely available on GitHub (https://github.com/kern-lab/discoal) under a GNU General Public License. CONTACT: kern@dls.rutgers.edu or dan.schrider@rutgers.eduSupplementary information: Supplementary data are available at Bioinformatics online.
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 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: discoal is implemented in the C programming language. Source code is freely available on GitHub (https://github.com/kern-lab/discoal) under a GNU General Public License. CONTACT: kern@dls.rutgers.edu or dan.schrider@rutgers.eduSupplementary information: Supplementary data are available at Bioinformatics online.
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