A Perl utility called SCANMS was written that operates on parametric bootstrap data generated by Hudsons simulator MS. SCANMS simulates sliding window analysis of Tajimas D or Fu and Lis D(*) or F(*) over the replicates and generates the empirical joint distribution of window minima and maxima. This distribution may then be used to calculate achieved significance values or significance cutoffs that account for multiple comparisons in sliding window analysis of real data.