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Bioinformatics. 2016 Jun 15;32(12):1895-7. doi: 10.1093/bioinformatics/btw051. Epub 2016 Feb 15.

SweepFinder2: increased sensitivity, robustness and flexibility.

Author information

1
Department of Biology and Institute for CyberScience, Pennsylvania State University, University Park, PA, USA.
2
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.
3
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA.
4
Department Biologie II, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany and.
5
Department of Integrative Biology, University of California, Berkeley, CA, USA.

Abstract

SweepFinder is a widely used program that implements a powerful likelihood-based method for detecting recent positive selection, or selective sweeps. Here, we present SweepFinder2, an extension of SweepFinder with increased sensitivity and robustness to the confounding effects of mutation rate variation and background selection. Moreover, SweepFinder2 has increased flexibility that enables the user to specify test sites, set the distance between test sites and utilize a recombination map.

AVAILABILITY AND IMPLEMENTATION:

SweepFinder2 is a freely-available (www.personal.psu.edu/mxd60/sf2.html) software package that is written in C and can be run from a Unix command line.

CONTACT:

mxd60@psu.edu.

PMID:
27153702
DOI:
10.1093/bioinformatics/btw051
[Indexed for MEDLINE]

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