Gautier, Mathieu, Klassmann, Alexander and Vitalis, Renaud ORCID: 0000-0001-7096-3089 (2017). REHH 2.0: a reimplementation of the R package REHH to detect positive selection from haplotype structure. Mol. Ecol. Resour., 17 (1). S. 78 - 91. HOBOKEN: WILEY. ISSN 1755-0998

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Abstract

Identifying genomic regions with unusually high local haplotype homozygosity represents a powerful strategy to characterize candidate genes responding to natural or artificial positive selection. To that end, statistics measuring the extent of haplotype homozygosity within (e.g. EHH, iHS) and between (Rsb or XP-EHH) populations have been proposed in the literature. The REHH package for R was previously developed to facilitate genome-wide scans of selection, based on the analysis of long-range haplotypes. However, its performance was not sufficient to cope with the growing size of available data sets. Here, we propose a major upgrade of the REHH package, which includes an improved processing of the input files, a faster algorithm to enumerate haplotypes, as well as multithreading. As illustrated with the analysis of large human haplotype data sets, these improvements decrease the computation time by more than one order of magnitude. This new version of REHH will thus allow performing iHS-, Rsb-or XP-EHH-based scans on large data sets. The package REHH 2.0 is available from the CRAN repository (http://cran.r-project.org/web/packages/rehh/index.html) together with help files and a detailed manual.

Item Type: Journal Article
Creators:
CreatorsEmailORCIDORCID Put Code
Gautier, MathieuUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Klassmann, AlexanderUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Vitalis, RenaudUNSPECIFIEDorcid.org/0000-0001-7096-3089UNSPECIFIED
URN: urn:nbn:de:hbz:38-243768
DOI: 10.1111/1755-0998.12634
Journal or Publication Title: Mol. Ecol. Resour.
Volume: 17
Number: 1
Page Range: S. 78 - 91
Date: 2017
Publisher: WILEY
Place of Publication: HOBOKEN
ISSN: 1755-0998
Language: English
Faculty: Unspecified
Divisions: Unspecified
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
HUMAN-POPULATIONS; HUMAN GENOME; SCANS; FOOTPRINTS; ADMIXTURE; PROGRAM; SIGNALSMultiple languages
Biochemistry & Molecular Biology; Ecology; Evolutionary BiologyMultiple languages
Refereed: Yes
URI: http://kups.ub.uni-koeln.de/id/eprint/24376

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