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.
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