SweepFinder2: increased sensitivity, robustness and flexibility

Michael DeGiorgio; Christian D Huber; Melissa J Hubisz; Ines Hellmann; Rasmus Nielsen

doi:10.1093/bioinformatics/btw051

SweepFinder2: increased sensitivity, robustness and flexibility

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

Authors

Michael DeGiorgio¹, Christian D Huber², Melissa J Hubisz³, Ines Hellmann⁴, Rasmus Nielsen⁵

Affiliations

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.

PMID: 27153702
DOI: 10.1093/bioinformatics/btw051

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.

MeSH terms

Evolution, Molecular
Humans
Likelihood Functions
Mutation Rate*
Selection, Genetic*
Software*