Run time and space performance as a function of input size. Each plot measures performance for fixed mutation rate θ - 0.5. Run time is measured in seconds processor time required per parameter value, averaged over 200 independent runs. Run time data is provided for our direct method (solid block line with circles), fastPHASE (dotted line with triangles), and haplotyper (dash-dot line with squares). Space usage is measured in maximum linear program size in variables × constraints over the full branch-and-bound execution, averaged over 200 independent runs, (a) Run time performance on 5-SNP windows, (b) Run time performance on 10-SNP windows, (c) Space usage on 5-SNP windows, (d) Space usage on 10-SNP windows.