To describe the relative computational burdens of these methods, we re-ran each program on a more limited dataset on a single Linux server, which had four dual-core Intel Xeon processors (running at 2.33 GHz, with a 6.1 MB cache, and using a 64-bit architecture) and a total of 8 GB of RAM. Specifically, we repeated the analysis for the 4th, 8th, 12th, and 16th chunks, each of which encompasses a 7.5 Mb region of chromosome 10 (centered, respectively, at positions 22.22 Mb, 50.22 Mb, 78.22 Mb, and 106.22 Mb in NCBI Build 35 coordinates). The average running times and memory requirements for these analyses are shown in Table 1.
