How does Dnadiff deal with gap penalties?
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23 months ago
caro-ca ▴ 20

Hi, community! For evaluating correctness, I aligned two similar draft assemblies using nucmer from MUMmer. To get the statistics of the alignment I used dnadiff. However, I do not know how the gap penalties work. I've been looking for literature, but there is nothing about dnadiff.

I hope you could recommend me some papers or help me out. Thanks in advance.

MUMmer dnadiff alignments gap penalties • 304 views
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