Aligns all pairs of sequences in a FASTA file using global alignment. Alignments are constructed and reported unconditionally; accept and termination conditions are not supported. Multithreading is not supported, though it could be implemented. You must either specify the -acceptall option, which aligns all pairs (except those for which no HSP is found), or accept options. See also: Example usearch -allpairs_global pairs.fasta
-alnout results.aln |