Aligns pairs of sequences in a FASTA file using local alignment. The first two sequences (1st and 2nd) are aligned, then the second pair (3rd and 4th) and so on up to the N-1th and Nth sequence. To align all-vs.-all, use allpairs_local. Alignments are constructed and reported unconditionally; accept and termination conditions are not supported. More than one alignment may be reported for a given pair. Multithreading is not supported, but this feature could be added.
Standard output file options
usearch -pairs_local pairs.fasta -alnout results.aln