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OmegaPlus specifications

Information


Unique identifier OMICS_08631
Name OmegaPlus
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained No

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Publication for OmegaPlus

OmegaPlus in publications

 (8)
PMCID: 5908061
PMID: 29672586
DOI: 10.1371/journal.pgen.1007311

[…] the power to detect positive selection and reduce the number of false positives []. currently, sweed [] is regarded as the most advanced clr-based test []. the ω statistic can be implemented by omegaplus []. to detect the common outliers of the sweed and omegaplus analyses, we ran r scripts available at http://pop-gen.eu/wordpress/server-for-selective-sweep-detection for the 2mb genomic […]

PMCID: 5745794
PMID: 29284515
DOI: 10.1186/s13059-017-1378-9

[…] for a false-positive rate of 0.01%. after filtering with the threshold of 27.85, the neighbor sweep targets were merged to sweep regions., to increase the ability to detect selective sweeps, omegaplus (version 2.3.0; a ld-based method) was used []. the ω statistic was computed at 10 kb intervals. the minwin and maxwin parameters were set to 10 kb and 100 kb, respectively. […]

PMCID: 5385031
PMID: 28405579
DOI: 10.1186/s40709-017-0064-0

[…] capacity to analyze whole genomes or just subgenomic regions. additionally, we summarize the results of comparisons among four open-source software releases (sweed, sweepfinder, sweepfinder2, and omegaplus) regarding sensitivity, specificity, and execution times. in equilibrium neutral models or mild bottlenecks, both sfs- and ld-based methods are able to detect selective sweeps accurately. […]

PMCID: 4880969
PMID: 27230431
DOI: 10.1186/s12863-016-0372-7

[…] tools: the ω statistic proposed by kim and nielsen [] was able to accurately localize the selective sweeps by a likelihood (ml) framework that uses linkage-disequilibrium (ld) information. omegaplus program [] has a high-performance implementation of the ω statistic at genome level and was utilized for scan to chromosome level the selective sweeps, with parameters -grid 47370, −minwin […]

PMCID: 4538300
PMID: 26347771
DOI: 10.3389/fgene.2015.00268

[…] population history may bias selection inference (e.g., ). further, recently evaluated several proposed background site frequency spectrum based approaches [including sweepfinder (), sweed (), omegaplus (), and ihs ()]. though they demonstrated the linkage disequilibrium based approaches to perform better, they also described a high false positive rate and low true positive rate […]


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OmegaPlus institution(s)
The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
OmegaPlus funding source(s)
Deutsche Forschungsgemeinschaft grant STA 860/2 (in part)

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