megablast 2.2.26 arguments: -d Database [String] default = nr -i Query File [File In] -e Expectation value [Real] default = 10.0 -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, 9 tabular with comment lines, 10 ASN, text 11 ASN, binary [Integer] default = 0 range from 0 to 11 -o BLAST report Output File [File Out] Optional default = stdout -F Filter query sequence [String] default = T -X X dropoff value for gapped alignment (in bits) [Integer] default = 20 -I Show GI's in deflines [T/F] default = F -q Penalty for a nucleotide mismatch [Integer] default = -3 -r Reward for a nucleotide match [Integer] default = 1 -v Number of database sequences to show one-line descriptions for (V) [Integer] default = 500 -b Number of database sequence to show alignments for (B) [Integer] default = 250 -D Type of output: 0 - alignment endpoints and score, 1 - all ungapped segments endpoints, 2 - traditional BLAST output, 3 - tab-delimited one line format, 4 - incremental text ASN.1, 5 - incremental binary ASN.1 [Integer] default = 2 -a Number of processors to use [Integer] default = 1 -O ASN.1 SeqAlign file; must be used in conjunction with -D2 option [File Out] Optional -J Believe the query defline [T/F] Optional default = F -M Maximal total length of queries for a single search [Integer] default = 5000000 -W Word size (length of best perfect match) [Integer] default = 28 -z Effective length of the database (use zero for the real size) [Real] default = 0 -Y Effective length of the search space (use zero for the real size) [Real] default = 0 -P Maximal number of positions for a hash value (set to 0 to ignore) [Integer] default = 0 -S Query strands to search against database: 3 is both, 1 is top, 2 is bottom [Integer] default = 3 -T Produce HTML output [T/F] default = F -l Restrict search of database to list of GI's [String] Optional -G Cost to open a gap (-1 invokes default behavior) [Integer] default = -1 -E Cost to extend a gap (-1 invokes default behavior) [Integer] default = -1 -s Minimal hit score to report (0 for default behavior) [Integer] default = 0 -Q Masked query output, must be used in conjunction with -D 2 option [File Out] Optional -f Show full IDs in the output (default - only GIs or accessions) [T/F] default = F -U Use lower case filtering of FASTA sequence [T/F] Optional default = F -R Report the log information at the end of output [T/F] Optional default = F -p Identity percentage cut-off [Real] default = 0 -L Location on query sequence [String] Optional -A Multiple Hits window size; default is 0 (i.e. single-hit extensions) or 40 for discontiguous template (negative number overrides this) [Integer] default = 0 -y X dropoff value for ungapped extension [Integer] default = 10 -Z X dropoff value for dynamic programming gapped extension [Integer] default = 50 -t Length of a discontiguous word template (contiguous word if 0) [Integer] default = 0 -g Make discontiguous megablast generate words for every base of the database (mandatory with the current BLAST engine) [T/F] Optional default = T -n Use non-greedy (dynamic programming) extension for affine gap scores [T/F] Optional default = F -N Type of a discontiguous word template (0 - coding, 1 - optimal, 2 - two simultaneous [Integer] default = 0 -H Maximal number of HSPs to save per database sequence (0 = unlimited) [Integer] default = 0 -V Force use of the legacy BLAST engine [T/F] Optional default = F