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               DNA WEIGHT MATRIX leads to a new menu where a single
               matrix (not a series) can be selected. The default is
               the matrix used by BESTFIT for comparison of nucleic
               acid sequences.

=head2 TYPE

 Title       : TYPE
 Description : (optional) sequence type: protein or DNA. This allows
                you to explicitly overide the programs attempt at
                guessing the type of the sequence.  It is only useful
                if you are using sequences with a VERY strange
                composition.

=head2 OUTPUT

 Title       : OUTPUT
 Description : (optional) clustalw supports GCG or PHYLIP or PIR or
                Clustal format.  See the Bio::AlignIO modules for
                which formats are supported by bioperl.