UNLABELLED: 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).
UNLABELLED: 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).
Authors: Lian Deng; Boon Peng Hoh; Dongsheng Lu; Ruiqing Fu; Maude E Phipps; Shilin Li; Ab Rajab Nur-Shafawati; Wan Isa Hatin; Endom Ismail; Siti Shuhada Mokhtar; Li Jin; Bin Alwi Zilfalil; Christian R Marshall; Stephen W Scherer; Fahd Al-Mulla; Shuhua Xu Journal: Hum Genet Date: 2014-06-11 Impact factor: 4.132
Authors: W Burgos-Paz; C A Souza; H J Megens; Y Ramayo-Caldas; M Melo; C Lemús-Flores; E Caal; H W Soto; R Martínez; L A Alvarez; L Aguirre; V Iñiguez; M A Revidatti; O R Martínez-López; S Llambi; A Esteve-Codina; M C Rodríguez; R P M A Crooijmans; S R Paiva; L B Schook; M A M Groenen; M Pérez-Enciso Journal: Heredity (Edinb) Date: 2012-12-19 Impact factor: 3.821
Authors: Ryan L Minster; Nicola L Hawley; Chi-Ting Su; Guangyun Sun; Erin E Kershaw; Hong Cheng; Olive D Buhule; Jerome Lin; Muagututi'a Sefuiva Reupena; Satupa'itea Viali; John Tuitele; Take Naseri; Zsolt Urban; Ranjan Deka; Daniel E Weeks; Stephen T McGarvey Journal: Nat Genet Date: 2016-07-25 Impact factor: 38.330