| allpairs_global | Compare all pairs of input sequences (local alignment). | |
| allpairs_local | Compare all pairs of input sequences (global alignment). | |
| calc_distmx | Calculate sparse distance matrix from sequences in FASTA file. | |
| cluster_agg | Agglomerative clustering of sequences. | |
| cluster_aggd | Agglomerative clustering using distance matrix. | |
| cluster_edges | Single-linkage clustering from graph edges in tabbed text file. | |
| cluster_fast | Cluster sequences, optimized for speed. | |
| cluster_otus | OTU clustering (UPARSE algorithm). | |
| cluster_smallmem | Cluster sequences, optimized for low memory use. | |
| depoly | Collapse long homopolymers. | |
| derep_fulllength | Dereplicate full-length sequences (find uniques). | |
| derep_prefix | Dereplicate (find uniques), allowing prefix matches. | |
| distmx2taxprobs | Create taxprobs file for utax. | |
| draw_tree | Make text "picture" from a tree in Phylip format. | |
| fasta_diversity | Report alpha diversity indexes and estimators. | |
| fasta_rarify | Calculate rarefaction curve from sequences in FASTA file. | |
| fastq_chars | Report statistics Q score ASCII characters in FASTQ file. | |
| fastq_eestats | Report expected-error statistics for FASTQ reads. | |
| fastq_filter | Quality filter FASTQ reads and/or convert to FASTA. | |
| fastq_join | Combine paired reads as R1-NNNNNN-RevComp(R2). | |
| fastq_mergepairs | Merge overlapping read pairs into single sequences ("contigs"). | |
| fastq_stats | Report statistics for FASTQ reads. | |
| fastx_findorfs | Find Open Reading Frames (ORFs) in FASTA or FASTQ file. | |
| fastx_getseq | Extract sequence with a given label from FASTA file. | |
| fastx_getseqs | Extract sequences from FASTA file. | |
| fastx_getsubseq | Extract subsequence. | |
| fastx_mask | Mask low-complexity regions in FASTA or FASTQ file. | |
| fastx_revcomp | Reverse complement sequences. | |
| fastx_split | Split FASTA or FASTQ file into approximately equal pieces. | |
| fastx_subsample | Generate a random subset of a FASTA or FASTQ file. | |
| fastx_truncate | Truncate FASTA or FASTQ sequences at fixed length. | |
| makeudb_ublast | Create database index for ublast command. | |
| makeudb_usearch | Create database index for usearch_global/local commands. | |
| pairs_global | Compare consecutive pairs of input sequences (global alignment). | |
| pairs_local | Compare consecutive pairs of input sequences (local alignment). | |
| sam_filter | Filter/convert SAM records. | |
| search_exact | Database search for 100% identical matches. | |
| search_global | Database search, global alignments. | |
| search_local | Database search (slow but thorough), local alignments. | |
| search_oligodb | Database search, database contains short nt. fragments. | |
| search_pcr | Find segments (predicted amplicons) matching a primer pair. | |
| search_peptidedb | Database search, database contains short a.a. fragments. | |
| sortbylength | Sort sequences by length. | |
| sortbysize | Sort sequences by abundance given as "size=N;" field in label. | |
| tree2clusters | Agglomerative clustering from a tree in Phylip format. | |
| tree2distmx | Calculate distance matrix from a tree in Phylip format. | |
| ublast | Database search, local alignments. | |
| uchime_denovo | Find chimeric sequences de novo (without ref db). | |
| uchime_ref | Find chimeric sequences using reference database. | |
| udb2fasta | Extract sequences from database index in FASTA format. | |
| udbinfo | Show parameters of database index file. | |
| udbstats | Report statistics for database index file. | |
| uparse_ref | Classify amplicon sequences using reference database. | |
| usearch_global | Database search, global alignments. | |
| usearch_local | Database search, local alignments. | |
| utax | Taxonomy assignment |