I want to use blastp to find out all the alignment among two fasta file.
Here is my command:
blastp -query "A.fasta" -subject "B.fasta" -evalue 1 -outfmt 6 > output.txt
I have already set the e-value tolerance to be 1, but there are still some alignments missing, is there anyway to force blastp to produce all the possible alignments?