SCANMS: Adjusting for multiple comparisons in sliding window neutrality tests

Abstract

A Perl utility called SCANMS was written that operates on parametric bootstrap data generated by Hudson's simulator MS. SCANMS simulates sliding window analysis of Tajima's D or Fu and Li's 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. © Oxford University Press 2004; all rights reserved.