Dear mauve-users,
I am trying to align sequences with a lot of ambiguous DNA bases (M, R, W,
S, Y, ...) with progressiveMauve and I was wondering how the tool is
handling these.
E.g. is the pair (A, M) considered a match or mismatch? How about (M, R)?
(M = A or C; R = A or G). Are ambigiuous bases even considered when
matching or are they replaced by "N" as with some other (alignment-) tools?
I tried to find my answer through the used substitution matrix but all
references to the HOXD matrix only contain A, T, C, G...
Thanks in advance,
Christine
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