WINDOWMIN is a window executable program used to determine the region of greatest discrimination between any given number of sequences. We will define the most discriminatory region, for a sample of size n, as the region that maximizes the number of different DNA sequences in a sample. It is possible to use different criteria for when two DNA sequence are defined to be different. For example, if sequencing errors are common, two DNA sequences may be defined to be different from each other if they differ at more than one nucleotide position. If sequencing errors can be ruled out, it may be more reasonable to define two DNA sequences as being different if they differ by in at least one nucleotide position. Let the number of different DNA sequences, distinguishable by at least k nucleotides, in a window starting in position i of the sequences, be nk,i. The window size considered must also be defined and is in the following assumed to be of size 600 bp. A window starting at position j in the sequence is then most discriminatory if nk,j = maxi{nk,i}for a particular value of k. If many possible windows fulfill this criteria, the procedure can be iterated to find the set of windows fulfilling nk+1,j = maxi{nk+1,i} among the sequences fulfilling nk,j = maxi{nk,i}. As a practical approach, we would iterate the algorithm 10 times and at this point choose the window with most segregating sites among the set of remaining windows.

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