rehh: Searching for Footprints of Selection using 'Extended Haplotype Homozygosity' Based Tests

Population genetic data such as 'Single Nucleotide Polymorphisms' (SNPs) is often used to identify genomic regions that have been under recent natural or artificial selection and might provide clues about the molecular mechanisms of adaptation. One approach, the concept of an 'Extended Haplotype Homozygosity' (EHH), introduced by (Sabeti 2002) <doi:10.1038/nature01140>, has given rise to several statistics designed for whole genome scans. The package provides functions to compute three of these, namely: 'iHS' (Voight 2006) <doi:10.1371/journal.pbio.0040072> for detecting positive or 'Darwinian' selection within a single population as well as 'Rsb' (Tang 2007) <doi:10.1371/journal.pbio.0050171> and 'XP-EHH' (Sabeti 2007) <doi:10.1038/nature06250>, targeted at differential selection between two populations. Various plotting functions are also included to facilitate visualization and interpretation of these statistics. Due to changes in the API, albeit mostly minor, versions 3.X are not compatible with versions 2.0.X. Note: optionally, vcf files can be imported using package vcfR. That package is currently removed from CRAN, but can still be installed from <> following instructions there.

Version: 3.1.2
Depends: R (≥ 2.10)
Imports: methods,
Suggests: ape, bookdown, data.table, gap, knitr, qqman, rmarkdown, R.utils, testthat, vcfR
Published: 2020-07-17
Author: Mathieu Gautier, Alexander Klassmann and Renaud Vitalis
Maintainer: Alexander Klassmann <rehh at>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: yes
Citation: rehh citation info
Materials: NEWS
CRAN checks: rehh results


Reference manual: rehh.pdf
Vignettes: Examples in detail
How to use rehh
Package source: rehh_3.1.2.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release: rehh_3.1.2.tgz, r-oldrel: rehh_3.1.2.tgz
Old sources: rehh archive

Reverse dependencies:

Reverse imports: coala


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