BlockFeST: Bayesian calculation of region-specific FST to detect local adaptation.

Abstract

The fixation index FST can be used to identify non-neutrally evolving loci from genome-scale SNP data across two or more populations. Recent years have seen the development of sophisticated approaches to estimate FST based on Markov-Chain Monte-Carlo simulations. Here, we present a vectorized R implementation of an extension of the widely used BayeScan software for codominant markers, adding the option to group individual SNPs into pre-defined blocks. A typical application of this new approach is the identification of genomic regions, genes, or gene sets containing SNPs that evolved under directional selection. The R implementation of our method, which builds on the powerful population genetics and genomics software PopGenome, is available freely from CRAN. Supplementary data are available at Bioinformatics online.