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 Description : Indicates the manner in which diagonals are scored
              during the fasta hashing.

              0 indicates that the score of a diagonal is equal to the
              sum of the scores of the exact matches it contains.


              1 indicates that this score is set equal to the score of
              the best uninterrupted segment

              1 can be useful when dealing with fragments of sequences.

=head2 SIM_MATRIX

 Title       : SIM_MATRIX
 Args        : string
 Default     : vasiliky
 Description : Indicates the manner in which the amino acid is being
               degenerated when hashing. All the substitution matrix
               are acceptable. Categories will be defined as sub-group
               of residues all having a positive substitution score