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