Cited by 553Genetic diversity and population structureGenetic and phenotypic traits in livestockGenetic Associations and Epidemiology

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rehh : an R package to detect footprints of selection in genome-wide SNP data from haplotype structure

Gautier, Mathieu, Vitalis, Renaud·2012·Bioinformatics

DOI 10.1093/bioinformatics/bts115

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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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Authors: Gautier, M., & Vitalis, R.
Affiliations: Centre de Biologie pour la Gestion des Populations (FR)
Centre National de la Recherche Scientifique (FR)
ORCID: Gautier, Mathieu
Vitalis, Renaud
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
DOI: 10.1093/bioinformatics/bts115
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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rehh : an R package to detect footprints of selection in genome-wide SNP data from haplotype structure

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