The complete arguments for BLASTALL 2.2.4

Program Name [String]
Database [String] default = nr
Query File [File In] default = stdin
Expectation value (E) [Real] default = 10.0
alignment view options: 0 = pairwise, 1 = query-anchored showing identities, 2 = query-anchored no identities, 3 = flat query-anchored, show identities, 4 = flat query-anchored, no identities, 5 = query-anchored no identities and blunt ends, 6 = flat query-anchored, no identities and blunt ends, 7 = XML Blast output, 8 = tabular, 9 tabular with comment lines [Integer] default = 0
BLAST report Output File [File Out] Optional default = stdout
Filter query sequence (DUST with blastn, SEG with others) [String] default = T
Cost to open a gap (zero invokes default behavior) [Integer] default = 0
Cost to extend a gap (zero invokes default behavior) [Integer] default = 0
X dropoff value for gapped alignment (in bits) (zero invokes default behavior) blastn 30, megablast 20, tblastx 0, all others 15 [Integer] default = 0
Show GI's in deflines [T/F] default = F
Penalty for a nucleotide mismatch (blastn only) [Integer] default = -3
Reward for a nucleotide match (blastn only) [Integer] default = 1
Number of database sequences to show one-line descriptions for (V) [Integer] default = 500
Number of database sequence to show alignments for (B) [Integer] default = 250
Threshold for extending hits, default if zero blastp 11, blastn 0, blastx 12, tblastn 13 tblastx 13, megablast 0 [Integer] default = 0
Perfom gapped alignment (not available with tblastx) [T/F] default = T
Query Genetic code to use [Integer] default = 1
DB Genetic code (for tblast[nx] only) [Integer] default = 1
Number of processors to use [Integer] default = 1
SeqAlign file [File Out] Optional
Believe the query defline [T/F] default = F
Matrix [String] default = BLOSUM62
Word size, default if zero (blastn 11, megablast 28, all others 3) [Integer] default = 0
Effective length of the database (use zero for the real size) [Real] default = 0
Number of best hits from a region to keep (off by default, if used a value of 100 is recommended) [Integer] default = 0
Effective length of the search space (use zero for the real size) [Real] default = 0
Query strands to search against database (for blast[nx], and tblastx) 3 is both, 1 is top, 2 is bottom [Integer] default = 3
Produce HTML output [T/F] default = F
Restrict search of database to list of GI's [String] Optional
Use lower case filtering of FASTA sequence [T/F] Optional default = F
X dropoff value for ungapped extensions in bits (0.0 invokes default behavior) blastn 20, megablast 10, all others 7 [Real] default = 0.0
X dropoff value for final gapped alignment in bits (0.0 invokes default behavior) blastn/megablast 50, tblastx 0, all others 25 [Integer] default = 0
PSI-TBLASTN checkpoint file [File In] Optional
MegaBlast search [T/F] default = F
Location on query sequence [String] Optional
Multiple Hits window size, default if zero (blastn/megablast 0, all others 40 [Integer] default = 0
Frame shift penalty (OOF algorithm for blastx) [Integer] default = 0
Length of the largest intron allowed in tblastn for linking HSPs (0 disables linking) [Integer] default = 0