{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T09:29:57Z","timestamp":1776331797036,"version":"3.50.1"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: 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.<\/jats:p>\n               <jats:p>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 \u2265 2).<\/jats:p>\n               <jats:p>Contact: \u00a0mathieu.gautier@supagro.inra.fr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts115","type":"journal-article","created":{"date-parts":[[2012,3,9]],"date-time":"2012-03-09T01:41:10Z","timestamp":1331257270000},"page":"1176-1177","source":"Crossref","is-referenced-by-count":496,"title":["<i>rehh<\/i>: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure"],"prefix":"10.1093","volume":"28","author":[{"given":"Mathieu","family":"Gautier","sequence":"first","affiliation":[]},{"given":"Renaud","family":"Vitalis","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2012,3,7]]},"reference":[{"key":"2023012711534855200_B1","doi-asserted-by":"crossref","first-page":"3128","DOI":"10.1111\/j.1365-294X.2011.05163.x","article-title":"Footprints of selection in the ancestral admixture of a new world creole cattle breed","volume":"20","author":"Gautier","year":"2011","journal-title":"Mol. Ecol."},{"key":"2023012711534855200_B2","article-title":"R: A Language and Environment for Statistical Computing","volume-title":"R Foundation for Statistical Computing","author":"R Development Core Team.","year":"2008"},{"key":"2023012711534855200_B3","doi-asserted-by":"crossref","first-page":"832","DOI":"10.1038\/nature01140","article-title":"Detecting recent positive selection in the human genome from haplotype structure","volume":"419","author":"Sabeti","year":"2002","journal-title":"Nature"},{"key":"2023012711534855200_B4","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1086\/502802","article-title":"A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase","volume":"78","author":"Scheet","year":"2006","journal-title":"Am. J. Hum. Genet."},{"key":"2023012711534855200_B5","doi-asserted-by":"crossref","first-page":"e171","DOI":"10.1371\/journal.pbio.0050171","article-title":"A new approach for using genome scans to detect recent positive selection in the human genome","volume":"5","author":"Tang","year":"2007","journal-title":"PLoS Biol."},{"key":"2023012711534855200_B6","doi-asserted-by":"crossref","first-page":"e72","DOI":"10.1371\/journal.pbio.0040072","article-title":"A map of recent positive selection in the human genome","volume":"4","author":"Voight","year":"2006","journal-title":"PLoS Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/8\/1176\/48930255\/bioinformatics_28_8_1176.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/8\/1176\/48930255\/bioinformatics_28_8_1176.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T12:15:14Z","timestamp":1674821714000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/8\/1176\/196491"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,3,7]]},"references-count":6,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2012,4,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts115","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2012,4]]},"published":{"date-parts":[[2012,3,7]]}}}