rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure.
Gautier, Mathieu 1; Vitalis, Renaud 2
[Miscellaneous Article] Bioinformatics. 28(8):1176-1177, April 15, 2012.

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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.

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).

Contact: [email protected]

Supplementary information: Supplementary data are available at Bioinformatics online.

(C) Copyright Oxford University Press 2012.