# The `Doublets` alphabet:

Doublets(nucleotide)

The `Doublets` alphabet is used for paired RNA stems.  The
alignment of Doublets partitions cannot be estimated.  It is
possible to estimate the alignment of loop regions while holding
the alignment of stems constant.  This makes sense, since RNA
stems are often more conserved than loops.

The nucleotides argument can be `DNA`, `RNA`, or missing.  If it
is missing, DNA or RNA is guessed based on frequency of
A,T,G,U, and C in the file.

# Examples:

   Doublets
   
   Doublets(RNA)
   
   Doublets(DNA)
