Inportant Options

-e, -ev: E-value limit. 10.0 if default.
-g: Gapped [T/F]. F if default.
-F: Filter query sequence (DUST with blastn, SEG with others) [String]. F if default.
-il: Identity cut-off. (0% id default.) [integer]
-mal: Minimum hit length. (Zero if default.) [integer]
-maxnum: Max number of plot. (No limit if default.) [integer]


blastmatrix options:
-il: Identity cut-off. (0% id default.) [integer]
-mal: Minimum hit length. (Zero if default.) [integer]
-maxnum: Max number of plot. (No limit if default.) [integer]
-xsize: Max width of the matrix. (640 dots if default.) [integer]
-ysize: Max hight of the matrix. (480 dots if default.) [integer]
-mu: Upper margin. (Automatic if default.) [integer]
-md: Lower margin. (Automatic if default.) [integer]
-mr: Right margin. (Automatic if default.) [integer]
-ml: Left margin. (Automatic if default.) [integer]

bl2seq 2.2.10 arguments:
-p Program name: blastp, blastn, blastx, tblastn, tblastx. For blastx 1st sequence should be nucleotide, tblastn 2nd sequence n
ucleotide [String]
-g Gapped [T/F]
default = F
-d theor. db size (zero is real size) [Real]
default = 0
-a SeqAnnot output file [File Out] Optional
-G Cost to open a gap (-1 invokes default behavior; non-default values can result in unreliable statistics) [Integer]
default = -1
-E Cost to extend a gap (-1 invokes default behavior; non-default values can result in unreliable statistics) [Integer]
default = -1
-X X dropoff value for gapped alignment (in bits) (zero invokes default behavior)
blastn 30, megablast 20, tblastx 0, all others 15 [Integer]
default = 0
-W Word size, default if zero (blastn 11, megablast 28, all others 3) [Integer]
default = 0
-M Matrix [String]
default = BLOSUM62
-q Penalty for a nucleotide mismatch (blastn only) [Integer]
default = -3
-r Reward for a nucleotide match (blastn only) [Integer]
default = 1
-F Filter query sequence (DUST with blastn, SEG with others) [String]
default = F
-e Expectation value (E) [Real]
default = 10.0
-S Query strands to search against database (blastn only). 3 is both, 1 is top, 2 is bottom [Integeqr]
default = 3
-T Produce HTML output [T/F]
default = F
-m Use Mega Blast for search [T/F] Optional
default = F
-Y Effective length of the search space (use zero for the real size) [Real]
default = 0
-t Length of the largest intron allowed in tblastn for linking HSPs [Integer]
default = 0
-I Location on first sequence [String] Optional
-J Location on second sequence [String] Optional
-D Output format: 0 - traditional, 1 - tabular [Integer]
default = 0
-U Use lower case filtering for the query sequence [T/F] Optional
default = F
-A Input sequences in the form of accession.version [T/F]
default = F
-V Force use of old engine [T/F] Optional
default = T