Bioinformatics· 2016Q1
S<scp>weep</scp>F<scp>inder</scp>2: increased sensitivity, robustness and flexibility
- 381citations
- Q1SCImago
- 2016year
Short summary
SweepFinder2, a new version of the SweepFinder software, offers increased sensitivity and robustness for detecting recent positive selection by accounting for mutation rate variation and background selection.
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Key points
- SweepFinder2 increases sensitivity and robustness for detecting recent positive selection.
- It accounts for mutation rate variation and background selection, which previously confounded results.
- Users can now specify test sites, set distances between them, and utilize recombination maps for greater flexibility.
AI-generated from the title and abstract; the full text is not read.
Abstract
UNLABELLED: 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.
The authors' abstract, as published at the source. Bioinformatics, 2016 · DOI ↗
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Field: Software
SoftwareComputer Science