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Protocols

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 citations

 (49)
call_split

Identifying artificial selection signals in the chicken genome

2018
PLoS One
PMCID: 5919632
PMID: 29698423
DOI: 10.1371/journal.pone.0196215
call_split See protocol

[…] calculates 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 that ha […]

library_books

Combining population genomics and fitness QTLs to identify the genetics of local adaptation in Arabidopsis thaliana

2018
Proc Natl Acad Sci U S A
PMCID: 5948977
PMID: 29686078
DOI: 10.1073/pnas.1719998115

[…] We used Sweepfinder2 () and the largest sample of accessions from each region (41 from Italy and 49 from Sweden; SI Appendix) to calculate CLR for recent selective sweeps. We estimated CLRs every 1 kb along t […]

call_split

Population genomics of finless porpoises reveal an incipient cetacean species adapted to freshwater

2018
Nat Commun
PMCID: 5893588
PMID: 29636446
DOI: 10.1038/s41467-018-03722-x
call_split See protocol

[…] To investigate the selection signals of wide-ridged and narrow-ridged forms of finless porpoises, we first scanned the genome for target regions of positive selection using Sweepfinder2, , which uses local deviations of the site frequency spectrum (SFS). The composite likelihood ratio (CLR) was estimated for each SNP and the top 20 genome “peaks” with a CLR higher than 0 […]

library_books

Genomic Signatures of Reinforcement

2018
Genes
PMCID: 5924533
PMID: 29614048
DOI: 10.3390/genes9040191

[…] summarized 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 and […]

library_books

Localization of adaptive variants in human genomes using averaged one dependence estimation

2018
Nat Commun
PMCID: 5818606
PMID: 29459739
DOI: 10.1038/s41467-018-03100-7

[…] To generate the receiver operating characteristic (ROC) curves for CMS, SweepFinder, and the component statistics (Fig. ), we varied the threshold for classifying a mutation as adaptive in order to cover the range from ~0% false-positive rate to ~100% true-positive rate. […]

library_books

RNA Interference Pathways Display High Rates of Adaptive Protein Evolution in Multiple Invertebrates

2018
Genetics
PMCID: 5887150
PMID: 29437826
DOI: 10.1534/genetics.117.300567

[…] erns of diversity and allele frequencies in the genomic region surrounding the selected site, and these can be used to detect recent adaptive substitutions (e.g., ; ; ). We used SweeD (; derived from Sweepfinder, ) to search for evidence of recent selective sweeps in the regions surrounding RNAi genes. The algorithm scans the genome and at a user-defined interval calculates the composite likelihoo […]


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

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