| Makes pair-wise all-vs.-all alignments of all pairs in a FASTA file. Alignments are local. No index is used. More than one alignment may be reported for a given pair. Alignments are reported unconditionally; accept options and termination options are not used. 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_local seqs.fasta -alnout
results.aln |