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allpairs_global command
Commands > Miscellaneous

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:
  Standard output file options
  Alignment parameters
  Alignment heuristics


usearch -allpairs_global pairs.fasta -alnout results.aln