title: rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure.
abstract: 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.
  
  
  METHODS
  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).
authors.affiliation: INRA, Montferrier-sur-Lez Cedex, France. mathieu.gautier@supagro.inra.fr
authors.forename: Mathieu
authors.initials: M
authors.lastname: Gautier
authors.forename: Renaud
authors.initials: R
authors.lastname: Vitalis
mesh_terms: D000818:Animals; D002417:Cattle; D055106:Genome-Wide Association Study; D006239:Haplotypes; D020641:Polymorphism, Single Nucleotide; D012984:Software