bkgd is a program for calculating B values across the genome. A B value is an estimate of the effect of background selection at a given site in the genome, given the recombination rate and density of sites under purifying selection.
genome is a python library for working with genomics data. It contains code for reading / writing HDF5 files that is based loosely on Michael Hoffman's genomedata format.
draw_genes is a program for plotting genomics data that is in HDF5 format. This code was used to generate figures for several papers including panels B & C of this figure; panel D of this figure; and panel B of this figure.