-------  ------------  --------------------
	program  query         database
	-------  ------------  --------------------
	fasta    DNA, protein  (same type as query)
	tfasta   protein       DNA
	lfasta   DNA, protein  (none)
	-------  ------------  --------------------

	 Specify databases for retrieving.  Specify one database or division
	name after keyword "datalib".  A division name is constructed by
	prefix + division, for example, ddbjbct, gbest, and so on.  If you
	specify a database name (for example, embl, swissprot, and so on),
	it means that you choose all the divisions of the database.  If you
	would like to retrieve from two or more databases or divisions, set
	two or more "datalib" lines.  You cannot omit this parameter.
	------------  -------  ------  -----------------------------------
	database      type     prefix  division
	------------  -------  ------  -----------------------------------
	ddbj          DNA      ddbj    bct est inv mam org pat phg pln pri
	                               rna rod sts syn una vrl vrt
	genbank       DNA      gb      bct est inv mam pat phg pln pri rna
	                               rod sts syn una vrl vrt
	embl          DNA      embl    est fun inv mam org pat phg pln pri
	                               pro rod sts syn unc vrl vrt
	swissprot     protein  (none)   (one division,  you can also use)
	                                (swiss or swiss-prot as the name)
	pir           protein  (none)  pir1 pir2 pir3 nrl_3d
	------------  -------  ------  ----------------------------------
	ddbjnew       DNA               (one division)
	gbnew         DNA               (one division)
	emblnew       DNA               (one division)
	swissnew      protein           (one division)
	------------  -------  ------  ----------------------------------

	 Specify K-tuple value.  This value determines how many consecutive
	identities ara requested in the estimation of a score for pairwise
	similarity.
	-------  -------  -------  -------
	query    minimum  maximum  default
	-------  -------  -------  -------
	DNA         1        6        6
	protein     1        2        2
	-------  -------  -------  -------

	 Specify the number of one-line summaries of names and scores in the
	output.  The default value is 20.

	 Specify the number of alignments to be displayed in the output.
	The default value is 20.

	 Specify scoring matrix.
	----------------  -------------------------------
	matrix            description
	----------------  -------------------------------
	codaa             minimum mutation matrix
	idnna             identity matrix
	idppa             identity matrix for mismatches,
	                    PAM250 matrix for matches
	pam120            PAM120 matrix
	pam250 (default)  PAM250 matrix
	----------------  -------------------------------

	 Specify the threshold to be used for optimization in a band around
	the best initial region.  By default, this value is calculated from
	the sequence length and the ktup value.

	 Specify the threshold for joining initial regions in the 2nd step of
	FASTA.  By default, this value is calculated from the sequence length
	and the ktup value.

	 Specify "on" or "off".  Option "on" forces to use score matrix (PAM)
	to identify initial regions.  If "off" is specified, constant score
	is used.  By default, this parameter sets "on" for protein sequences,
	"off" for DNA sequences.

	Specify the style of alignment.
	-----------  --------  ------------  ---------
                               conservative  mismatch
	mode         identity     change      or gap
	-----------  --------  ------------  ---------
	0 (default)     :           .        (space)
	1            (space)        x           X
	2               .       (residue)    (residue)
	-----------  --------  ------------  ---------
	Example:
	----------    ----------    ----------
	 MARKX=0       MARKX=1       MARKX=2
	----------    ----------    ----------
	MWRTCGPPYT    MWRTCGPPYT    MWRTCGPPYT
	::..:: :::      xx  X       ..KS..Y...
	MWKSCGYPYT    MWKSCGYPYT
	----------    ----------    ----------

 	 Selection "on" shows the complete sequence instead of just the overlap
	of the two aligned sequences.  The default is "off".

	 Selection "on" scales similarity scores by ln(n0)/ln(n1), where n0
	and n1 are the length of the query and library sequences.  Unscaled
	scores are shown with the alignment, though.  The default is "off".

	 Selection "off" omits a histogram in the output.  The default
	is "on".

         If the query or database sequences are > 85% (A+C+G+T), the sequence is
	assumed a DNA.  If you wish to force the query sequence to be treated
	as a DNA, specify this option "on".  The default is "off".

	 Selection "on" inverts (reverse complement) the query sequence if it is
	a DNA.  The default is "off".

	 Selection "on" sorts the summary of output by init1 score.  The default
	is "off".

toporf
	 This option is only for "tfasta" program.  Selection "on" forces to
	translate only three forward frames.  The default is "off".