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discoal: flexible coalescent simulations with selection

Andrew D. Kern, Daniel R. Schrider
doi: https://doi.org/10.1101/063453
Andrew D. Kern
1Department of Genetics, Rutgers University, Piscataway, NJ, 08854, USA
2Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, 08554, USA
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Daniel R. Schrider
2Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, 08554, USA
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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

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted July 12, 2016.
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discoal: flexible coalescent simulations with selection
Andrew D. Kern, Daniel R. Schrider
bioRxiv 063453; doi: https://doi.org/10.1101/063453
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discoal: flexible coalescent simulations with selection
Andrew D. Kern, Daniel R. Schrider
bioRxiv 063453; doi: https://doi.org/10.1101/063453

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