| makeudb_sintax | Create database index for sintax | |
| makeudb_ublast | Create database index for ublast | |
| makeudb_usearch | Create database index for usearch_global and uchime | |
| orient | Orient nt sequences to the same strand as a database | |
| search_exact | Search for full-length identical database sequences | |
| search_global | Search database (global alignments, no index) | |
| search_local | Search database (local alignments, no index) | |
| search_oligodb | Find matches to short nt sequences e.g. primers | |
| search_pcr | Search for amplicons (matches to primer pairs) | |
| search_peptidedb | Find matches to short a.a. sequences e.g. peptides | |
| search_phix | Screen input for matches to PhiX genome | |
| ublast | Fast database search (local alignment similar to BLAST) | |
| udb2fasta | Extract sequences from UDB file | |
| udbinfo | Report index parameters used to make UDB file | |
| usearch_global | Fast database search (indexed, global alignment) | |
| usearch_local | Fast database search (indexed, local alignment) |