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Mauve is most effective when used on genomes that are similar in length. Multiple genomes that are too different in length can end up with short alignments to one or more of the reference genomes.
Two Mauve parameters are important in minimizing the effect of trivial initial alignments: a minimum percent identity parameter and a minimum percent identity parameter on split alignments. The percent identity parameter lessens the effect of regions near the ends of genomes that are difficult to align because they have little sequence similarity. The ec5d62056f burnnans
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