Rehh

Rehh detects genomic regions showing signatures of selection by analyzing haplotype homozygosity in SNP haplotype datasets.

Key Features:

• Haplotype homozygosity analysis: Implements analysis of haplotype homozygosity to identify regions with elevated local homozygosity relative to neutral expectations.
• Genome-wide scans: Performs genome-wide scans of long-range haplotypes across whole genomes using SNP haplotype datasets.
• Detection of recent and ongoing selection: Detects footprints of both recent and ongoing selection events.
• Graphical functions: Provides graphical functions for visualization of haplotype homozygosity and scan results.
• Support for model and non-model species: Operates on SNP haplotype data from both model and non-model species, including datasets generated by next-generation sequencing and genotyping.

Scientific Applications:

• Detection of selection signals: Identification of genomic regions and candidate genes under natural or artificial selection by detecting elevated haplotype homozygosity.
• Evolutionary and population genetics: Study of recent adaptive evolution and population genetic patterns using long-range haplotype information.
• Conservation genomics: Prioritization of loci relevant to conservation biology by detecting adaptive variation.
• Functional genomics: Linking selection footprints to putative functional or phenotypic effects for downstream functional studies.

Methodology:

Computes haplotype homozygosity and performs genome-wide scans of long-range haplotypes in SNP haplotype datasets to identify regions with unusually high local homozygosity compared to neutral expectations, and produces graphical visualizations of results.