Home Software Services About Contact     

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.


usearch -allpairs_local seqs.fasta -alnout results.aln