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allpairs_local command
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:
  Standard output file options
  Alignment parameters
  Alignment heuristics


usearch -allpairs_local seqs.fasta -alnout results.aln