How to specify stop codons and frame shifts in the alignment.

    - In-frame stop codons:
        * or _
 
        Examples: 
          NGDLP*PQLKN or NGDLP_PQLKN


    - Frame shifts:
        by number

        Examples:
          Gene1   HCDGE
          Gene2   HC1GE    only 1 nuc residue.

          Gene1   HCDGE
          Gene2   HC2GE    only 2 nuc residues.

          Gene1   ND-TY
          Gene2   ND1TY    1 nuc residue inserted.

          Gene1   ND-TY
          Gene2   ND2TY    2 nuc residues inserted.

          Gene1   EREQK
          Gene2   EK4QK    1 nuc residue inserted.