Natural selection for the Duffy-null allele in the recently admixed people of Madagascar AUTHORS: Jason A. Hodgson, Imperial College London, j.hodgson@imperial.ac.uk Joseph K. Pickrell, New York Genome Center Laurel N. Pearson, Penn State University Ellen E. Quillen, Texas Biomedical Research Institute António Prista, Universidade Pedagogica, Mozambique Jorge Rocha, Uiversidade do Porto Himla Soodyall, University of Witwatersrand Mark D. Shriver, Penn State University George H. Perry, Penn State University The following files are contained here: DATA: Samples were genotyped with the Affymetrix GeneChip Human 10k 2.0 SNP array. Data files are in PLINK binary format. If text files are desired, execute the files in PLINK and export the desired file type. Hodgson_etal_Data.bed Hodgson_etal_Data.bim Hodgson_etal_Data.fam SAMPLE INFORMATION: Hodgson_etal_Sample_Information.txt COMPUTER PROGRAM: fastadsim.pl This program simulates genetic drift of an allele given various population parameters. The program should run on any computer with a Perl interpreter, however it has only been tested on Mac OS X. For questions, problems, or updates to the software, contact: Jason Hodgson Dept. of Life Sciences Imperial College London j.hodgson@imperial.ac.uk Program usage: This is a command line program that requires a series of arguments to execute properly. On a Macintosh, follow the following steps: 1. Open a terminal session and navigate to the directory containing the executable file. 2. Make sure the program is executable. Type: chmod +x fastadsim.pl 3. For example, to run the program type: ./fastadsim.pl -g 100 -k 1.10 -l 0 -a 0.48 -m1 2 -m2 0 -n 100 -p1 0 -p2 1 -s 10000 -o results.txt This will perform 10,000 simulations of genetic drift for the given parameters, recording the final allele frequency each time. Results are written to results.txt The available parameters are: -g number of generations of admixture -k population growth parameter -l number of generations prior to population growth -a admixture proportion of population 1 at generation 0 -m1 migration rate of population 1 per generation -m2 migration rate of population 2 per generation -n effective population size of generation 0 -p1 allele 1 frequency of population 1 -p2 allele 1 frequency of population 2 -s number of simulations to run -o outfile name