[Mauve-users] DNA ambiguity codes

[Christine J. <chr...@gm...>]

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