![]() When I trace back by hand I end up with AAAc because I only visit the Ic matrix once. So in the final output the alignment of ZZ to AAAC should be AAac. These sequences are being recorded in the a2m format, where inserts in the sequence are recorded as a lower case character. ![]() The edge case I am having a problem with is when the bottom right score is not in the match matrix, but is in the insert column matrix (meaning that the resulting traced back sequence should have a insert. The idea is that in order to re construct the sequence (the longest path) we re-calculate to determine the matrix the score came from. I almost have my needleman-wunsch implementation working but I am confused on how to handle the traceback on a specific case.
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