Run time was measured on a Linux cluster using one core on a node equipped with 24 GB RAM and two Intel Xeon L5520 processors running on 2.26 GHz. Time for performing association analyses for 1000 subjects and 1000 replicates (similar to 1000 genetic variants in our study) was recorded. For TATES and UV-MA, run time also included the time used for UV association analyses of the three traits. MV-BIMBAM was the fastest method using 9 seconds, while PCHAT needed 437 minutes and 15 seconds. Run times for MV-PLINK, MV-SNPTEST, MultiPhen, TATES, UV-PCA and UV-MA were 23 seconds, 1 minute and 10 seconds, 3 minutes and 18 seconds, 23 seconds, 23 seconds and 19 seconds, respectively.
