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USEARCH v11

allpairs_global command

See also
  Standard output file options
  Alignment parameters
  Alignment heuristics

Aligns all pairs of sequences in a FASTA file using global alignment.

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_global pairs.fasta -alnout results.aln