| Option | Definition | Type | Default |
| -a | Number of processors to use. | [Integer] | 1 |
| -b | Number of database sequence to show alignments for (B). | [Integer] | 250 |
| -d | Database: multiple database names are bracketed by quotations, for example : -d "db1 db2 db3". | [String] | nr |
| -e | Expectation value (E). | [Real] | 10.0 |
| -f | Threshold for extending hits, default if 0. | [Integer] | 0 |
| -g | Perfom gapped alignment (not available with tblastx). | [T/F] | T |
| -i | Query File. | [File In] | stdin |
| -l | Restrict search of database to list of GIs. | [String] | Optional |
| -m | Alignment view options: - 0 = Tairwise.
- 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.
| [Integer] | 0 |
| -n | MegaBLAST search. | [T/F] | F |
| -o | BLAST report Output File. | [File Out] | stdout |
| -p | Program Name. | [String] | |
| -q | Penalty for a nucleotide mismatch (blastn only). | [Integer] | -3 |
| -r | Reward for a nucleotide match (blastn only). | [Integer] | 1 |
| -v | Number of database sequences to show one-line descriptions for (V). | [Integer] | 500 |
| -y | Dropoff (X) for blast extensions in bits (0.0 invokes default behavior). | [Real] | 0.0 |
| -z | Effective length of the database (use 0 for the real size). | [Real] | 0 |
| -A | Multiple Hits window size (0 for single-hit algorithm). | [Integer] | 40 |
| -D | DB Genetic code (for tblast[nx] only). | [Integer] | 1 |
| -E | Cost to extend a gap (0 invokes default behavior). | [Integer] | 0 |
| -F | Filter query sequence (DUST with blastn, SEG with others). | [String] | T |
| -G | Cost to open a gap (0 invokes default behavior). | [Integer] | 0 |
| -I | Show GIs in deflines. | [T/F] | F |
| -J | Believe the query defline. | [T/F] | F |
| -K | Number of best hits from a region to keep (off by default; if used, a value of 100 is recommended). | [Integer] | 0 |
| -L | Location on query sequence. | [String] | |
| -M | Matrix. | [String] | BLOSUM62 |
| -O | SeqAlign file. | [File Out] | |
| -P | - 0 = Multiple hits, 1-pass.
- 1 = Single hit, 1-pass.
- 2 = 2-pass.
| [Integer] | 0 |
| -Q | Query Genetic code to use. | [Integer] | 1 |
| -R | PSI-TBLASTN checkpoint file. | [File In] | |
| -S | Query strands to search against database (for blast[nx], and tblastx). 3 is both, 1 is top, 2 is bottom. | [Integer] | 3 |
| -T | Produce HTML output. | [T/F] | F |
| -U | Use lower case filtering of FASTA sequence. | [T/F] | F |
| -W | Word size, default if 0. | [Integer] | 0 |
| -X | X dropoff value for gapped alignment (in bits) (0 invokes default behavior). | [Integer] | 0 |
| -Y | Effective length of the search space (use 0 for the real size). | [Real] | 0 |
| -Z | X dropoff value for final gapped alignment (in bits). | [Integer] | 0 |
