The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
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 (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
Citations
Cites
R: A Language and Environment for Statistical Computing
R Core Team (2000) · doi:10.32614/r.manuals · Cited by 355,893
A Map of Recent Positive Selection in the Human Genome
Voight, B. F., Kudaravalli, S., Wen, X., & Pritchard, J. K. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040072 · Cited by 2,925
Detecting recent positive selection in the human genome from haplotype structure
Sabeti, P. C., Reich, D. E., Higgins, J. M., Levine, H. Z. P., Richter, D. J., Schaffner, S. F., Gabriel, S. B., Platko, J. V., Patterson, N. J., McDonald, G. J., et al. (2002) · Nature · doi:10.1038/nature01140 · Cited by 2,106
Scheet, P. A., & Stephens, M. (2006) · The American Journal of Human Genetics · doi:10.1086/502802 · Cited by 1,959
A new approach for using genome scans to detect recent positive selection in the human genome
Tang, K., Thornton, K. R., & Stoneking, M. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050171 · Cited by 489
Footprints of selection in the ancestral admixture of a New World Creole cattle breed
Gautier, M., & Navès, M. (2011) · Molecular Ecology · doi:10.1111/j.1365-294x.2011.05163.x · Cited by 168
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selscan: An Efficient Multithreaded Program to Perform EHH-Based Scans for Positive Selection
Szpiech, Z. A., & Hernandez, R. D. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu211 · Cited by 805
Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon
Barson, N. J., Aykanat, T., Hindar, K., Baranski, M., Bolstad, G. H., Fiske, P., Jacq, C., Jensen, A. J., Johnston, S. E., Karlsson, S., et al. (2015) · Nature · doi:10.1038/nature16062 · Cited by 663
Comparative genetic architectures of schizophrenia in East Asian and European populations
Schizophrenia Working Group of the Psychiatric Genomics Consortium, Lam, M., Indonesia Schizophrenia Consortium, Genetic REsearch on schizophreniA neTwork-China and the Netherlands (GREAT-CN), Chen, C.-Y., Li, Z., Martin, A. R., Bryois, J., Ma, X., Gaspar, H., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0512-x · Cited by 655
The genomic landscape underlying phenotypic integrity in the face of gene flow in crows
Poelstra, J. W., Vijay, N., Bossu, C. M., Lantz, H., Ryll, B., Müller, I., Baglione, V., Unneberg, P., Wikelski, M. C., Grabherr, M. G., et al. (2014) · Science · doi:10.1126/science.1253226 · Cited by 551
The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication
Wang, M., Yu, Y., Haberer, G., Marri, P. R., Fan, C., Goicoechea, J. L., Zuccolo, A., Song, X., Kudrna, D., Ammiraju, J. S. S., et al. (2014) · Nature Genetics · doi:10.1038/ng.3044 · Cited by 425
Metadata
- 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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