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Discoal: flexible coalescent simulations with selection.

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.

SUBMITTER: Kern AD

PROVIDER: S-EPMC5167068 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature

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Discoal: flexible coalescent simulations with selection.

Kern Andrew D AD Schrider Daniel R DR

Bioinformatics (Oxford, England) 20160824 24

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 ...[more]

PMID: 27559153

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