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code for estimating the effect of background selection
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This repository contains code for estimating the strength of background selection. This software was written by Graham McVicker and is described in detail in the methods section of our paper, McVicker et al. 2009: http://dx.plos.org/10.1371/journal.pgen.1000471 Some additional mathematical details are provided in the file bkgd_selection.pdf. If you have any questions about the software please contact me at: email@example.com calc_bkgd --------- The calc_bkgd program computes the reduction in neutral diversity due to background selection (B-values) at every site in a genome. As input the program takes a recombination map, a list of chromosomes to run on, and the locations of elements that are believed to be under purifying selection. All of the options for the program are provided through a configuration file. An example file that explains all of the options is provided in the conf/calc_bkgd.conf calc_bkgd depends on glib-2.x (http://developer.gnome.org/glib/) for several data structures (e.g. hashtables, linked lists, stacks), and on the gnu scientific library (http://www.gnu.org/software/gsl/) for numerical integration and function minimization. Both of these software libraries must be installed before calc_bkgd can be compiled. To compile: cd bkgd make bkgd_mle -------- This program uses the B-values computed by calc_bkgd and a multi-species sequence alignment to perform maximum likelihood estimation of evolutionary parameters such as mutation rates, deleterious mutation rates, effective population sizes, and speciation times. The program is written specifically for multiple alignments of human, chimp, gorilla, orangutan macaque genome sequences, but could probably be adapted to other purposes. Currently this program is not built by the makefile. Contact me if you are interested in using this part of the code and I can help get you started. Data ---- Precomputed B-values for the human genome are provided in the data directory.