zalpha: an R package for the identification of regions of the genome under selection.

Detecting evidence of selection and evolution in population genomes is crucial to understanding the history and the selective pressures experienced by a population. While there are many statistics for identifying regions of the genome under selection, there is a need for software to enable reproducible, standardised results. The statistics implemented in the zalpha R package use the relationships and correlations in genetic variation to find patterns that could be indicative of a selective sweep. The methods contained within this R package are a development of the statistics published by Jacobs et al. (2016). This package allows users to run a range of selection statistics on genetic data, which previously were not made publicly available in software. The software is designed to be flexible to allow users to efficiently combine statistics and is open source. The package also allows users to utilise a linkage disequilibrium (LD) profile, taking into ac-count expected relationships between alleles, ultimately increasing the power of the statistics. This is important as LD varies immensely along the genome, with recombination the biggest contributor to LD fluctuations (Jeffreys et al., 2001)