afsource.tar

This file contains source code for computer software that implements the allele frequency model described in the manuscript. Please e-mail [e-mail] for additional details, and full documentation will likely be released on-line in the future. 1. The software depend on the Gnu Scientific Library. The software can be compiled using the g++ compiler as follows (this assumes the GSL was isntalled in a standard location), g++ -o af main.C func.C -lm -lgsl -lgslcblas 2. You can view command line arguments to the software by typing the name of the compiled binary. The infile format is similar to the infile format for bgc. 3. Three output files are produced. One contains the posterior probabilities for the genotype at each locus for each individual (gprob). A second file contains a matrix with samples from the posterior probability distribution for the allele frequencies (afreq) with each row corresponding to an mcmc iteration and each column corresponding to a locus. The final file (alpha) contains samples from the posterior probability distribution of the genetic diversity parameter.