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Old 02-08-2015, 09:31 AM   #2
Brian Bushnell
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Location: Walnut Creek, CA

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I performed a global pairwise alignment of my sequences using needle (Needleman-Wunsch algorithm) from the Emboss package, which is known to produces an optimal alignment.
Needleman-Wunsch does not yield optimal alignments. For optimality, under a model that assumes fewer mutation events are more likely than more mutation events, you need affine transforms to encourage insertions or deletions to be made adjacent rather than scattered around at random, which Needleman-Wunsch or Smith-Waterman will do because they are greedy algorithms.

That's just an aside, though. I don't know what tools would help you in this case.
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