The HGDP selection browser created and maintained by Joe Pickrell, which accompanies our paper on signals of selection in the Human Genome Diversity Panel (Pickrell et a. 2009)
Supplementary Data for Coop et al. High-resolution mapping of crossovers reveals extensive variation in fine-scale recombination patterns among humans.
Bayenv
Loci involved in local adaptation can potentially be identified by an unusual correlation between allele frequencies and important ecological variables, or by extreme allele frequency differences between geographic regions. However, such comparisons are complicated by differences in sample sizes and the neutral correlation of allele frequencies across populations due to shared history and gene flow. To overcome these difficulties, we have developed a Bayesian method that estimates the empirical pattern of covariance in allele frequencies between populations from a set of markers, and then uses this as a null model for a test at individual SNPs. I developed this method in collaboration with David Witonsky, Anna Di Rienzo and Jonathan K. Pritchard. The method is described in a paper in Genetics. The program and various related files are available here.
SelSim
Chris Spencer and Graham developed SelSim a program to simulate sequence, SNP or microsatellite data for a recombining sequence with a single selected site. The model of selection is a general biallelic scheme. The program is available from Chris’s new website. The program is described in SelSim: A program to simulate population genetic data with selection and recombination.
Sel_Genetree
This is an implementation of the importance sampling method discussed in Ancestral inference on gene trees under selection, available on request from Graham.
