convert aln.trimmed_alignment to aln.trimmed and a little cleanup
Fix error with trimming external alignments

When trimming alignments from other programs (e.g. SATe), ensure
that the sequence we are trimming has the correct alphabet.  For
whatever reason, reading in alignments was setting the alphabet
to SingleLetterAlphabet, which is incompatible with
IUPAC.ambiguous_dna.  So, enure that alphabet is IUPAC.ambiguous_dna.