| Search for one (default) or a few high-identity hits to a database using the USEARCH algorithm. Alignments are global. To get more than one hit, increase -maxaccepts. An identity threshold must be specified using the ‑id option. A database file must be specified using the ‑db option. FASTA and .udb formats are supported. For large databases, .udb format is recommended (see makeudb_usearch command). The ‑strand option is required for nucleotide databases. Nucleotide, protein and translated searches are supported. See also: Examples usearch -usearch_global query.fasta -db
proteins.udb -id 0.8 -alnout results.aln |