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search_global command
Comprehensive database search. All database sequences are aligned to the query, no index is used. Alignments are global. Much slower than usearch_global for large datasets; mostly useful for ad hoc queries on small datasets. Sensitive to arbitrarily low identities.

An identity threshold must be specified using the ‑id option.

A database file must be specified using the ‑db option.

The ‑strand option is required for nucleotide databases.

Nucleotide, protein and translated searches are supported.

See also:
  Standard output file options
Accept options
  Weak hits
  Termination options
  Alignment parameters
  Alignment heuristics


usearch -search_global query.fasta -db db.fasta -id 0.9 -alnout results.aln