I'm wondering if there is any software or algorithms, given a set of
DNA sequences to find a maximally divergent segment (of length N) in
each sequence so when aligned to all other sequences it is of the
highest divergence. Most people are looking for similiarities but I'd
like to do this!! I guess that I could use blast, but that would give
me similarities. I tried flipping scores for matches and mismatches
but it did not quite work!!
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