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SweepFinder specifications

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Unique identifier OMICS_08599
Name SweepFinder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for SweepFinder

SweepFinder in publications

 (43)
PMCID: 5919632
PMID: 29698423
DOI: 10.1371/journal.pone.0196215

[…] the likelihood ratio of selection signals by comparing the spatial distribution of allele frequencies in an observed window to the frequency spectrum of the whole genome. in this analysis, sweepfinder [] software was employed to calculate the clr with a grid size of 10 kb. to explore ongoing selection signals, the ihs method was performed, which searches for haplotype structures […]

PMCID: 5948977
PMID: 29686078
DOI: 10.1073/pnas.1719998115

[…] cn qtl (2:1) contained windows with significantly elevated proportions of snps correlated to climate ( and si appendix, fig. s3 b–e)., using composite likelihood ratio (clr) tests (implemented in sweepfinder2), we identified genomic regions with significant evidence of recent selective sweeps in italy and sweden (). we also identified regions that showed significant increases in linkage […]

PMCID: 5893588
PMID: 29636446
DOI: 10.1038/s41467-018-03722-x

[…] footprints of positive selection in finless porpoises that might be related to these differences, we used the recent improved version of the composite likelihood ratio (clr) test implemented in sweepfinder2. we identified 218 genes and 144 candidate genes embedded in 39 clr peaks with strong selective sweep signals in wide- and narrow-ridged form populations, respectively (fig. , […]

PMCID: 5924533
PMID: 29614048
DOI: 10.3390/genes9040191

[…] using statistics such as tajima’s d [], fay and wu’s h [], ω-statistic [], and integrated haplotype score (ihs) [] that are calculated and analyzed across the genome using programs such as sweepfinder2 [], sweepd [], and omegaplus []. the predicted signature may vary depending on the evolutionary history of the alleles under selection (see for a discussion on variation between soft […]

PMCID: 5818606
PMID: 29459739
DOI: 10.1038/s41467-018-03100-7

[…] for measuring population differentiation, integrated haplotype score (ihs) for identifying shared haplotypes, and tajima’s d for detecting deviations from the neutral sfs. some approaches, like sweepfinder and sweed integrate information across sites by modeling changes to the sfs. often, statistical scans for adaptive mutations proceed by choosing a particular genomic signature […]


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SweepFinder institution(s)
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA

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