bl2seq (BLAST 2 Sequences) allows for the alignment of two given sequences.
The following table summarizes the bl2seq options.
| Option | Definition | Type | Default |
| -a | SeqAnnot output file. | [File Out] | |
| -d | Theoretical database size (0 is real size). | [Integer] | 0 |
| -e | Expectation value (E). | [Real] | 10.0 |
| -g | Gapped. | [T/F] | T |
| -i | First sequence. | [File In] | |
| -j | Second sequence. | [File In] | |
| -m | Use MegaBLAST for search. | [T/F] | F |
| -o | Alignment output file. | [File Out] | stdout |
| -p | Program name: blastp, blastn, blastx, tblastn, tblastx. For blastx, the first sequence should be nucleotide; for tblastn, the 2nd sequence sequence should be nucleotide. | [String] | |
| -q | Penalty for a nucleotide mismatch (blastn only). | [Integer] | -3 |
| -r | Reward for a nucleotide match (blastn only). | [Integer] | 1 |
| -t | Length of the largest intron allowed in tblastn for linking HSPs. | [Integer] | 0 |
| -A | Input sequences in the form of <accession.version>. | [T/F] | F |
| -D | Output format: 0 = traditional; 1 = tabulated. | [Integer] | 0 |
| -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 | Location on first sequence. | [String] | |
| -J | Location on second sequence. | [String] | |
| -M | Matrix. | [String] | BLOSUM62 |
| -S | Query strands to search against database (blastn only). 3 is both, 1 is top, 2 is bottom. | [Integer] | 3 |
| -T | Produce HTML output. | [T/F] | F |
| -U | Use lowercase filtering for the query sequence. | [T/F] | F |
| -W | Wordsize (0 invokes default behavior). | [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 |