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USEARCH v11

allpairs_local command

See also
  Standard output file options
  Alignment parameters
  Alignment heuristics

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.

You must either specify the -acceptall option, which aligns all pairs (except those for which no HSP is found), or accept options.

Example

usearch -allpairs_local seqs.fasta -alnout results.aln