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Old 11-09-2011, 10:26 AM   #3
NGS specialist
Location: Malaysia

Join Date: Apr 2008
Posts: 249

Novoalign does support gap open and gap extension penalties. Finding the right balance of these with your data is something you might think about doing. The defaults are set quite conservatively as with most other tools that perform a similar function.
Also do remember that allowing more gaps/mismatches can potentially drop your specificity.
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