How does DefineClones deal with non-nuc characters

[Namita Gupta]

Finally, for some reason my file has a few locations where the junction is recorded as the string "None", and this was being treated as an actual junction.

[Namita Gupta]

Now any character not considered in your given model's distance matrix (e.g., IUPAC ambiguous DNA for hamming, 'ACGTN.-' for hs5f) will give an error when trying to look up the distance in the model's distance matrix.