docs: def aa_frequencies(seq, gap_chars='-.'):
      """Calculate the amino acid frequencies in a sequence set."""
      aa_counts = Counter(seq)
      # Don't count gaps
      for gap_char in gap_chars:
          if gap_char in aa_counts:
              del aa_counts[gap_char]
      # Reduce to frequencies
      scale = 1.0 / sum(aa_counts.values())
      return dict((aa, cnt * scale) for aa, cnt in aa_counts.iteritems())