| Option | Definition | Type | Default |
| -a | Number of processors to use. | [Integer] | 1 |
| -b | Number of database sequence to show alignments for (B). | [Integer] | 250 |
| -c | Constant in pseudocounts for multipass version. | [Integer] | 9 |
| -d | Database. | [String] | nr |
| -e | Expectation value (E). | [Real] | 10.0 |
| -f | Threshold for extending hits. | [Integer] | 0 |
| -g | Gapped. | [T/F] | T |
| -h | e-value threshold for inclusion in multipass model. | [Real] | 0.005 |
| -i | Query File. | [File In] | stdin |
| -j | Maximum number of passes to use in multipass version. | [Integer] | 1 |
| -k | Hit File for PHI-BLAST. | [File In] | hit_file |
| -l | Restrict search of database to list of GIs. | [String] | |
| -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 = qQuery-anchored no identities and blunt ends.
- 6 = Flat query-anchored, no identities and blunt ends.
- 7 = XML Blast output.
- 8 = Tabular output.
| [Integer] | 0 |
| -o | Output file for alignment. | [File Out] | stdout |
| -p | Program option for PHI-BLAST. | [String] | blastpgp |
| -s | Compute locally optimal Smith-Waterman alignments. | [T/F] | F |
| -t | Tweak Lambda, K, and score matrix for each match. | [T/F] | T |
| -v | Number of database sequences to show one-line descriptions for (V). | [Integer] | 500 |
| -y | Dropoff (X) for blast extensions in bits (default if 0). | [Real] | 7.0 |
| -z | Effective length of the database (use 0 for the real size). | [Integer] | 0 |
| -A | Multiple hits window size (0 for single-hit algorithm). | [Integer] | 40 |
| -B | Input alignment file for PSI-BLAST restart. | [File In] | |
| -C | Output file for PSI-BLAST checkpointing. | [File Out] | |
| -E | Cost to extend a gap. | [Integer] | 1 |
| -F | Filter query sequence with SEG. | [String] | F |
| -G | Cost to open a gap. | [Integer] | 11 |
| -H | End of required region in query (-1 indicates end of query). | [Integer] | -1 |
| -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. | [Integer] | 0 |
| -L | Cost to decline alignment (disabled when 0). | [Integer] | 0 |
| -M | Matrix. | [String] | BLOSUM62 |
| -N | Number of bits to trigger gapping. | [Real] | 22.0 |
| -O | SeqAlign file ("Believe the query defline" must be TRUE). | [File Out] | Optional |
| -P | - 0 = Multiple hits, 1-pass.
- 1 = Single hit, 1-pass.
- 2 = 2-pass.
| [Integer] | 0 |
| -Q | Output file for PSI-BLAST matrix in ASCII. | [File Out] | |
| -R | Input file for PSI-BLAST restart. | [File In] | |
| -S | Start of required region in query. | [Integer] | 1 |
| -T | Produce HTML output. | [T/F] | F |
| -U | Use lowercase filtering of FASTA sequence. | [T/F] | F |
| -W | Word size, default if 0. | [Integer] | 0 |
| -X | X dropoff value for gapped alignment (in bits). | [Integer] | 15 |
| -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] | 25 |
