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 Description : (optional) number of best diagonals to use
               The number of k-tuple matches on each diagonal
               (in an imaginary dot-matrix plot) is calculated.
               Only the best ones (with most matches) are used in
               the alignment.  This parameter specifies how many.
               Decrease for speed; increase for sensitivity.

=head2 WINDOW

 Title       : WINDOW
 Description : (optional) window size
               This is the number of diagonals around each of the 'best'
               diagonals that will be used.  Decrease for speed;
               increase for sensitivity.

=head2 PAIRGAP

 Title       : PAIRGAP
 Description : (optional) gap penalty for pairwise alignments
               This is a penalty for each gap in the fast alignments.
               It has little affect on the speed or sensitivity except
               for extreme values.

=head2 FIXEDGAP

 Title       : FIXEDGAP
 Description : (optional) fixed length gap penalty

=head2 FLOATGAP

 Title       : FLOATGAP
 Description : (optional) variable length gap penalty

=head2 MATRIX

 Title       : MATRIX
 Default     : PAM100 for DNA - PAM250 for protein alignment
 Description : (optional) substitution matrix used in the multiple
               alignments. Depends on the version of clustalw as to
               what default matrix will be used

               PROTEIN WEIGHT MATRIX leads to a new menu where you are
               offered a choice of weight matrices. The default for
               proteins in version 1.8 is the PAM series derived by
               Gonnet and colleagues. Note, a series is used! The
               actual matrix that is used depends on how similar the
               sequences to be aligned at this alignment step
               are. Different matrices work differently at each
               evolutionary distance.

               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.

=head2 OUTFILE

 Title       : OUTFILE
 Description : (optional) Name of clustalw output file. If not set
                module will erase output file.  In any case alignment will
                be returned in the form of SimpleAlign objects

=head2 TRANSMIT

 Title       : TRANSMIT
 Description : (optional) transitions not weighted.  The default is to
                weight transitions as more favourable than other
                mismatches in DNA alignments.  This switch makes all
                nucleotide mismatches equally weighted.

=head2 program_name

 Title   : program_name
 Usage   : $factory>program_name()
 Function: holds the program name
 Returns:  string
 Args    : None

=head2 program_dir

 Title   : program_dir
 Usage   : $factory->program_dir(@params)
 Function: returns the program directory, obtained from ENV variable.
 Returns:  string
 Args    :

=head2 version

 Title   : version
 Usage   : exit if $prog->version() < 1.8
 Function: Determine the version number of the program
 Example :
 Returns : float or undef
 Args    : none

=head2 run

 Title   : run
 Usage   : ($aln, $tree) = $factory->run($inputfilename);
           ($aln, $tree) = $factory->run($seq_array_ref);
 Function: Perform a multiple sequence alignment, generating a tree at the same
           time. (Like align() and tree() combined.)
 Returns : A SimpleAlign object containing the sequence alignment and a
           Bio::Tree::Tree object with the tree relating the sequences.
 Args    : Name of a file containing a set of unaligned fasta sequences