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selscan 2.0: scanning for sweeps in unphased data

View ORCID ProfileZachary A. Szpiech
doi: https://doi.org/10.1101/2021.10.22.465497
Zachary A. Szpiech
1Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
2Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA 16802, USA
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  • ORCID record for Zachary A. Szpiech
  • For correspondence: szpiech@psu.edu
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Abstract

Haplotype-based scans to identify recent and ongoing positive selection have become commonplace in evolutionary genomics studies of numerous species across the tree of life. However, the most widely adopted approaches require phased haplotypes to compute the key statistics. Here we release a major update to the selscan software that re-defines popular haplotype-based statistics for use with unphased “multi-locus genotype” data. We provide unphased implementations of iHS, nSL, XP-EHH, and XP-nSL and evaluate their performance across a range of important parameters in a generic demographic history. Source code and executables are available at https://www.github.com/szpiech/selscan.

Competing Interest Statement

The authors have declared no competing interest.

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-ND 4.0 International license.
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Posted October 24, 2021.
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selscan 2.0: scanning for sweeps in unphased data
Zachary A. Szpiech
bioRxiv 2021.10.22.465497; doi: https://doi.org/10.1101/2021.10.22.465497
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selscan 2.0: scanning for sweeps in unphased data
Zachary A. Szpiech
bioRxiv 2021.10.22.465497; doi: https://doi.org/10.1101/2021.10.22.465497

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