title: SweepFinder2: increased sensitivity, robustness and flexibility.
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.
  
  
  
  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.
  
  
  
  mxd60@psu.edu.
authors.affiliation: Department of Biology and Institute for CyberScience, Pennsylvania State University, University Park, PA, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: DeGiorgio
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.
authors.forename: Christian D
authors.initials: CD
authors.lastname: Huber
authors.affiliation: Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA.
authors.forename: Melissa J
authors.initials: MJ
authors.lastname: Hubisz
authors.affiliation: Department Biologie II, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany and.
authors.forename: Ines
authors.initials: I
authors.lastname: Hellmann
authors.affiliation: Department of Integrative Biology, University of California, Berkeley, CA, USA.
authors.forename: Rasmus
authors.initials: R
authors.lastname: Nielsen
mesh_terms: D019143:Evolution, Molecular; D006801:Humans; D016013:Likelihood Functions; D059645:Mutation Rate; D012641:Selection, Genetic; D012984:Software