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PipMaker computes alignments of similar regions in two DNA sequences. The resulting alignments are summarized with a “percent identity plot”, or “pip” for short. MultiPipMaker allows the user to see relationships among more than two sequences. All pairwise alignments with the first sequence are computed and then returned as interleaved pips. Moreover, MultiPipMaker can be requested to compute a true multiple alignment of the input sequences and return a nucleotide-level view of the results.
