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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 citations

 (12)
library_books

Selection on the regulation of sympathetic nervous activity in humans and chimpanzees

2018
PLoS Genet
PMCID: 5908061
PMID: 29672586
DOI: 10.1371/journal.pgen.1007311

[…] rease 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 regi […]

library_books

Genomic Signatures of Reinforcement

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

[…] 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 hard sweeps). Importantly, unde […]

library_books

Adaptation of Arabidopsis thaliana to the Yangtze River basin

2017
Genome Biol
PMCID: 5745794
PMID: 29284515
DOI: 10.1186/s13059-017-1378-9

[…] , allowing 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. As in the Fastsi […]

call_split

A survey of methods and tools to detect recent and strong positive selection

2017
PMCID: 5385031
PMID: 28405579
DOI: 10.1186/s40709-017-0064-0
call_split See protocol

[…] t neutrality when using Tajima’s D on 1-kb windows, while rejecting neutrality when using the same summary statistic on 2-kb windows. More advanced tests, such as SweepFinder/SweepFinder2, SweeD, and OmegaPlus implement variable-sized windows (see below). While evaluating windows of varying sizes does not solve the problem completely, due to the inevitable existence of lower and upper bounds for t […]

library_books

Rare intronic variants of TCF7L2 arising by selective sweeps in an indigenous population from Mexico

2016
BMC Genet
PMCID: 4880969
PMID: 27230431
DOI: 10.1186/s12863-016-0372-7

[…] ole-genome 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 1 […]

call_split

Scalable linkage disequilibrium based selective sweep detection: a performance guide

2016
GigaScience
PMCID: 4746822
PMID: 26862394
DOI: 10.1186/s13742-016-0114-9
call_split See protocol

[…] mputations between very distant SNPs. SNPs are placed in groups based on their alignment site index to facilitate the application of the proposed algorithm directly on the data layout of the standard OmegaPlus implementation. Fig. 4 […]


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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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