Additional argument should be provided in the following format: [argument_name] [argument_value] Accepted argument_names includes: -f Threshold for extending hits [Integer] default = 11 -m 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 output, 9 = Tabular output with comments 10 = ASN, text 11 = ASN, binary [Integer] default = 0 -y Dropoff (X) for blast extensions in bits (default if zero) [Real] default = 7.0 -P 0 for multiple hit, 1 for single hit [Integer] default = 0 -G Cost to open a gap [Integer] default = 11 -E Cost to extend a gap [Integer] default = 1 -X X dropoff value for gapped alignment (in bits) [Integer] default = 15 -N Number of bits to trigger gapping [Real] default = 22.0 -h e-value threshold for inclusion in multipass model [Real] default = 0.002 -c Constant in pseudocounts for multipass version; 0 uses entropy method; otherwise a value near 30 is recommended [Integer] default = 0 -j Maximum number of passes to use in multipass version [Integer] default = 1 -J Believe the query defline [T/F] default = F -Z X dropoff value for final gapped alignment (in bits) [Integer] default = 25 -O SeqAlign file ('Believe the query defline' must be TRUE) [File Out] Optional -M Matrix [String] default = BLOSUM62 -W Word size [Integer] default = 3 -z Effective length of the database (use zero for the real size) [Real] default = 0 -K Number of best hits from a region to keep [Integer] default = 0 -s Compute locally optimal Smith-Waterman alignments [T/F] default = F -Y Effective length of the search space (use zero for the real size) [Real] default = 0 -U Use lower case filtering of FASTA sequence [T/F] Optional default = F -t Use composition based score adjustment As first character: 0 or F or f: no composition-based statistics 2 or T or t: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties in round 1 1: Composition-based statistics as in NAR 29:2994--3005, 2001 3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally in round 1 As second character, if first character is equivalent to 1, 2, or 3: U or u: unified p-value combining alignment p-value and compositional p-value in round 1 only [String] default = 2 -L Cost to decline alignment (disabled when 0) [Integer] default = 0