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    (quadratic in memory and time)

    myers_miller_pair_wise : implementation of the Myers and Miller
    dynamic programming algorithm ( quadratic in time and linear in
    space). This algorithm is recommended for very long sequences. It
    is about 2 time slower than gotoh. It only accepts tg_mode=1.

    fasta_pair_wise: implementation of the fasta algorithm. The
    sequence is hashed, looking for ktuples words. Dynamic programming
    is only carried out on the ndiag best scoring diagonals. This is
    much faster but less accurate than the two previous.

    cfasta_pair_wise : c stands for checked. It is the same
    algorithm. The dynamic programming is made on the ndiag best
    diagonals, and then on the 2*ndiags, and so on until the scores
    converge. Complexity will depend on the level of divergence of the
    sequences, but will usually be L*log(L), with an accuracy
    comparable to the two first mode ( this was checked on BaliBase).

=head2 KTUPLE

 Title       : KTUPLE
 Args        : numeric value
 Default     : 1 or 2 (1 for protein, 2 for DNA )

 Description : Indicates the ktuple size for cfasta_pair_wise dp_mode
               and fasta_pair_wise. It is set to 1 for proteins, and 2
               for DNA. The alphabet used for protein is not the 20
               letter code, but a mildly degenerated version, where
               some residues are grouped under one letter, based on
               physicochemical properties:
               rk, de, qh, vilm, fy (the other residues are
               not degenerated).

=head2 NDIAGS

 Title       : NDIAGS
 Args        : numeric value
 Default     : 0
 Description : Indicates the number of diagonals used by the
               fasta_pair_wise algorithm. When set to 0,
               n_diag=Log (length of the smallest sequence)

=head2 DIAG_MODE

 Title       : DIAG_MODE
 Args        : numeric value
 Default     : 0


 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
               (they can overlap).

               If you wish to keep the non degenerated amino acid
               alphabet, use 'idmat'

=head2 MATRIX

 Title       : MATRIX
 Args        :
 Default     :
 Description : This flag is provided for compatibility with
               ClustalW. Setting matrix = 'blosum' is equivalent to
               -in=Xblosum62mt , -matrix=pam is equivalent to
               in=Xpam250mt . Apart from this, the rules are similar
               to those applying when declaring a matrix with the
               -in=X fl

=head2 GAPOPEN

 Title       : GAPOPEN
 Args        : numeric
 Default     : 0
 Description : Indicates the penalty applied for opening a gap. The
               penalty must be negative. If you provide a positive
               value, it will automatically be turned into a negative
               number. We recommend a value of 10 with pam matrices,
               and a value of 0 when a library is used.

=head2 GAPEXT

 Title       : GAPEXT
 Args        : numeric
 Default     : 0
 Description : Indicates the penalty applied for extending a gap.

=head2 COSMETIC_PENALTY

 Title       : COSMETIC_PENALTY
 Args        : numeric
 Default     : 100
 Description : Indicates the penalty applied for opening a gap. This
               penalty is set to a very low value. It will only have
               an influence on the portions of the alignment that are
               unalignable. It will not make them more correct, but
               only more pleasing to the eye ( i.e. Avoid stretches of
               lonely residues).

               The cosmetic penalty is automatically turned off if a
               substitution matrix is used rather than a library.