SweeD: likelihood-based detection of selective sweeps in thousands of genomes.

ABSTRACT: The advent of modern DNA sequencing technology is the driving force in obtaining complete intra-specific genomes that can be used to detect loci that have been subject to positive selection in the recent past. Based on selective sweep theory, beneficial loci can be detected by examining the single nucleotide polymorphism patterns in intraspecific genome alignments. In the last decade, a plethora of algorithms for identifying selective sweeps have been developed. However, the majority of these algorithms have not been designed for analyzing whole-genome data. We present SweeD (Sweep Detector), an open-source tool for the rapid detection of selective sweeps in whole genomes. It analyzes site frequency spectra and represents a substantial extension of the widely used SweepFinder program. The

SUBMITTER: Pavlidis P 

PROVIDER: S-EPMC3748355 | biostudies-literature | 2013 Sep

REPOSITORIES: biostudies-literature