INRA, INRA-CNRS, UMR CBGP (INRA - IRD - Cirad - Montpellier SupAgro), Campus International de Baillarguet, CS 30016, F-34988 Montferrier-sur-Lez Cedex, France.
With the development of next-generation sequencing and genotyping approaches, large SNP haplotype data sets 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 , which provides a versatile tool to detect the footprints of recent or ongoing selection, thanks to several graphical functions that help visual interpretation of the results.
rehh is available for Windows, Mac OS X and Linux platforms from http://www1.montpellier.inra.fr/URLB/Rpackages/rehh_1.0_all.zip. Function documentation and example data files are provided within the package and a tutorial is available as supplementary information. rehh is distributed under the GNU General Public Licence (GPL ≥ 2).