# The `--alphabet` command:

-A         [partitions:]<alphabet>          The alphabet.
--alphabet [partitions:]<alphabet>

The alphabet can be:

   `DNA`, `RNA`, `Amino-Acids`, `Numeric`, `Doublets`,
   `Triplets`, or `Codons`

If no partitions are specified, then the alphabet is applied to
every partition.  The `--alphabet` command can be given multiple times,
but the same partition cannot be referenced twice.

The Doublets alphabet takes an optional extra argument specifying
the nucleotide alphabet:

     Doublets[DNA]            Doublets[RNA]

The Triplets and Codons alphabets take optional
extra arguments specifying the nucleotide alphabet and genetic code:

     Triplets[DNA]            Codons[RNA,standard]

# Examples:

   --alphabet=DNA
   -A RNA
   --alphabet=1,3:DNA --alphabet=2:Codons

# See also:

   alphabets, Triplets, Codons, Doublets
