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SHR Neuro Cancer Cardio Lipid Metab Microb

Pfeifer, B; Lercher, MJ.
BlockFeST: Bayesian calculation of region-specific FST to detect local adaptation.
Bioinformatics. 2018; 34(18): 3205-3207. Doi: 10.1093/bioinformatics/bty299 [OPEN ACCESS]
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Leading authors Med Uni Graz: Pfeifer Bastian
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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.