Calculate Single Site B

Bvalcalc --site --pop_params Params.py

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

Core Arguments

--pop_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.
--gene_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 (MBE). 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.
--quiet: Suppress console output

Bvalcalc --site --pop_params HumanParams.py --distance 1500 --gene_size 10000

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