fgwas. Software for incorporating functional genomic information into genome-wide association studies.
TreeMix. TreeMix infers trees and graphs of populations from allele frequency data.
RNA-seq software. Some scripts for analysis of RNA-seq data.
Selection software. Scripts for calculating iHS (by Sridhar Kudaravalli), XP-EHH, and forward simulations with selection. 


HGDP Selection Browser. Contains the genotype data and results from Pickrell et al. (2009) and Coop et al. (2009). 
eQTL Resources. Contains the RNA-seq data and results from Pickrell et al. (2010).