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Bioinformatics. 2012 Apr 15;28(8):1176-7. doi: 10.1093/bioinformatics/bts115. Epub 2012 Mar 7.

rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure.

Author information

1
INRA, Montferrier-sur-Lez Cedex, France. mathieu.gautier@supagro.inra.fr

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.

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).

PMID:
22402612
DOI:
10.1093/bioinformatics/bts115
[Indexed for MEDLINE]

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