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MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools.

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percent identity plot (bot) compared with gene models (top)
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percent-identity color coded dotplot of a promer alignment
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unordered multiplot of finished vs. draft sequence alignment
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ordered and oriented multiplot of finished vs. draft seqs

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