In the current un-optimized implementation of the weighted-sum method, a genome wide analysis of 20,000 groups, with 50 polymorphic variants each, using nA = nU = 1000 individuals can be completed in approximately 600 CPU hours on a standard stand-alone machine (Intel Pentium Dual 2 GHz, 2GB RAM). When the number of permutations (k) is 500 instead of 1000, the results are unaffected (results not shown) but the computing time is halved, however since the test is fast we use k = 1000 in this study. Note that the computation time is linear in number of individuals and number of permutations (see Table S3).
