Calculate Single Site B

Bvalcalc --site --params Params.py

--site: Calculate B for a single site at a specified distance from a single selected element

Core Arguments

--params [path/to/YourParams.py]: Path to a Python file defining population genetic parameters, see here for accessing pre-built templates, Generate Parameters, and here for adjusting parameters to new species/populations, Tailoring Parameters.
--element_size [int]: Total length of the selected region, e.g. gene or CDS, (default: 10000)
--distance [int]: Distance from the focal neutral site to the edge of the selected element in bp (default: 1). Note that this assumes recombinant distance increases linearly with physical distance.

--pop_change: If included, compute current B (Bcur) under a step population size change, as described in Johri et al. (2021). Note that Bcur and time_of_change should be set in the parameters file when active.
--gamma_dfe: If included, use a gamma distribution to define the DFE (instead of fixed f0, f1, f2, f3). Note that mean, shape and proportion_synonymous should be set in the parameters file when active.
--constant_dfe: If included, use a constant fixed s value as the DFE of selected sites (instead of fixed f0, f1, f2, f3). Note that s and proportion_synonymous should be set in the parameters file when active.
--quiet: Suppress console output

Bvalcalc --site --params HumanParams.py --distance 1500 --element_size 10000

# B for site 1500bp away from 10000bp region: 0.9670029436948963

Calculates B for a single site 1500bp away from a gene under selection of length 10kb using example human parameters.