DefineClones bygroup --model aa does not support gaps in the sequence

[Jason Vander Heiden]

Might just need a change to either the translate function's table argument or the Seq object's alphabet. See Bio.Data.CodonTable and Bio.Alphabet.IUPAC.ExtendedIUPACProtein

[Namita Gupta]

gaps are now temporarily changed to Ns and get translated correctly to Xs