The B-value calculator: expected diversity under background selection

Background selection (BGS), resulting from indirect effects of selection at linked and unlinked conserved sites experiencing purifying selection, is a key evolutionary force that shapes patterns of diversity across genomes. Calculating the expected diversity at neutral sites under BGS relative to that under strict neutrality (referred to as B-value or simply B) is important for understanding processes that shape patterns of genomic variation and for developing null models when performing inference, in particular, demographic inference and detection of selective sweeps. We extend and integrate previous theory to estimate B-values analytically, assuming no selective interference. Here, we present the B-value calculator, Bvalcalc, an easy-to-use command-line interface written in Python for efficient analytical calculation of expected B genome-wide at single base-pair resolution. Bvalcalc has several modules for calculating diversity as a function of distance from a single conserved element or considering the multiplicative effects of all conserved elements across the genome, accounting for recombination maps, gene conversion, self-fertilization, single population size changes, and unlinked effects from other chromosomes, where specified. We validated the effectiveness of Bvalcalc with comparisons against simulated results, and generated B-maps for the model species Homo sapiens, Drosophila melanogaster and Arabidopsis thaliana as a proof of concept using public data. Bvalcalc is available with documentation at johrilab.github.io/Bvalcalc/.