rehh : an R package to detect footprints of selection in genome-wide SNP data from haplotype structure
Abstract
Unlabelled With the development of next-generation sequencing and genotyping approaches, large single nucleotide polymorphism haplotype datasets are becoming available in a growing number of both model and non-model species. Identifying genomic regions with unexpectedly high local haplotype homozygosity relatively to neutral expectation represents a powerful strategy to ascertain candidate genes responding to natural or artificial selection. To facilitate genome-wide scans of selection based on the analysis of long-range haplotypes, we developed the R package rehh. It provides a versatile tool to detect the footprints of recent or ongoing selection with several graphical functions that help visual interpretation of the results. Availability and implementation Stable version is available from CRAN: http://cran.r-project.org/. Development version is available from the R-forge repository: http://r-forge.r-project.org/projects/rehh. Both versions can be installed directly from R. Function documentation and example data files are provided within the package and a tutorial is available as Supplementary Material. rehh is distributed under the GNU General Public Licence (GPL ≥ 2).
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Under positive selection, strong and long range linkage disequilibrium and unexpectedly high local haplotype homozygosity might occur in the genome.
“Under positive selection, strong and long range linkage disequilibrium (LD) and unexpectedly high local haplotype homozygosity might occur in the genome (Gautier and Vitalis, 2012; Bomba et al., 2015).”
From Identification of Candidate Signature Genes and Key Regulators Associated With Trypanotolerance in the Sheko Breed (2019) · cites this paper as Gautier and Vitalis, 2012
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- Authors
- Gautier, M., & Vitalis, R.
- Affiliations
- Centre de Biologie pour la Gestion des Populations (FR)
- Centre National de la Recherche Scientifique (FR)
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-03-07
- Volume
- 28
- Issue
- 8
- Pages
- 1176-1177
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2112358885
- Cited by
- 528
- References
- 6
- Citations by year
- 2026: 44 · 2025: 58 · 2024: 65 · 2023: 42 · 2022: 58 · 2021: 47 · 2020: 29 · 2019: 22 · 2018: 33 · 2017: 30 · 2016: 21 · 2015: 43 · 2014: 21 · 2013: 12 · 2012: 2
- FWCI
- 15.18
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- selection signatures, haplotype homozygosity, single nucleotide polymorphisms, haplotype structure, genome scan, candidate genes, R package
- MeSH terms
- Animals, Cattle, Haplotypes, Software, Polymorphism, Single Nucleotide, Genome-Wide Association Study
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