SCANMS is an open source utility written in Perl that works in conjunction with Richard Hudson’s coalescent simulator MS to do parametric bootstrapping of a sliding window analysis of neutrality test statistics.
SDSW (Sliding Divergence Sequence Window) needs a set of ALIGNED FASTA format sequences (at least two; gap character ‘-‘) as input and computes pairwise mismatch values for sliding windows of a given size, with a given step size. This is done for every pair of sequences in the input file, and, in addition, average values across all pairs are calculated. Calculations are done in two ways: (a) ignoring comparisons of a nucleotide chararcter with a gap character (N/-) in the mismatch, or (b) including it (more details in the accompanying pdf). The output is written as tab-delimited text.
GrASP (Graphical Assessment of Sliding P-values) is a graphical tool to display and assess p-values from sliding window tests. It can present thousands of p-values from the sliding window tests as a simple graphic that uses varying levels of user-specified color to indicate the width of the sliding windows and the varying levels of significance. It therefore allows the user to identify regions/blocks of interest from these sliding windows, based jointly on the absolute p-value of the tests from these windows and the building of haplotypes of significance in the region. GrASP is executed as an Excel macro and is written in Excel’s built-in version of Visual Basic for Applications.
