| allpairs_global | All-vs-all global alignment | |
| allpairs_local | All-vs-all local alignment | |
| alpha_div | Calculate alpha diversity metrics | |
| alpha_div_rare | Calculate alpha diversity metrics with rarefaction (subsampling) | |
| annot | Annotate sequences as known, contaminant or chimeric | |
| beta_div | Calculate beta diversity metrics | |
| calc_distmx | Calculate distance matrix | |
| calc_distmx_smallmem | Calculate distance matrix using memory-saving method | |
| closed_ref | OTU assignment by database matching | |
| cluster_agg | Agglomerative clustering, input is sequences | |
| cluster_aggd | Agglomerative clustering, input is distance matrix | |
| cluster_edges | Construct connected components from graph edges | |
| cluster_fast | Greedy clustering (UCLUST algorithm) | |
| cluster_otus | OTU clustering with chimera filtering (UPARSE-OTU algorithm) | |
| cluster_smallmem | Greedy clustering (UCLUST algorithm) | |
| derep_fulllength | Find unique sequences and abundances (old name for fastx_uniques) | |
| draw_tree | Converts tree to human-readable text file | |
| fasta_explode | Split FASTA into one file per sequence | |
| fasta_stripgaps | Strip gap characters from sequences | |
| fastq_chars | Reports frequencies of Phred (Q) scores in FASTQ file | |
| fastq_eestats | Expected error distribution in FASTQ file (long report) | |
| fastq_eestats2 | Expected error distribution in FASTQ file (short report) | |
| fastq_filter | Quality filter FASTQ and/or convert reads to FASTA format. | |
| fastq_join | Concatenate forward (R1) and reverse (R2) reads | |
| fastq_mergepairs | Merge (assemble) paired reads with overlaps | |
| fastq_sra_splitpairs | Recover R1 and R2 reads from SRA interleaved or concatenated format | |
| fastx2qiime | Convert sample names to QIIME-compatible format | |
| fastx_demux | Assign reads to samples using index reads (demultiplex) | |
| fastx_findorfs | Find Open Reading Frames (ORFs) in FASTX file | |
| fastx_getlabels | Get labels from FASTA/Q file | |
| fastx_getseq | Extract sequence(s) by label from FASTX file | |
| fastx_getseqs | Extract sequence(s) by label from FASTX file | |
| fastx_getsubseq | Extract subsequence by label and start-stop coordinates from FASTX file | |
| fastx_info | Summarize contents of FASTX file | |
| fastx_learn | Estimate error rates for amplicon reads | |
| fastx_mask | Low-complexity masking | |
| fastx_relabel | Re-label FASTA/Q sequences | |
| fastx_revcomp | Reverse-complement nucleotide sequences | |
| fastx_split | Split FASTX file into two or more roughly equal-size pieces | |
| fastx_strip_annots | Strip annotations from labels | |
| fastx_subsample | Extract random subset of sequences in a FASTX file | |
| fastx_truncate | Truncate sequences | |
| fastx_uniques | Find unique sequences and abundances | |
| fastx_uniques_persample | Find unique sequences and abundances per sample | |
| filter_phix | Filter PhiX sequences | |
| 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 | |
| otutab | Create OTU table | |
| otutab2biom | Convert tabbed-text OTU table to BIOM v1 format | |
| otutab_counts2freqs | Convert OTU table from counts to frequencies. | |
| otutab_freqs2counts | Convert OTU table from frequencies to counts | |
| otutab_group | Combine samples into groups | |
| otutab_merge | Merge two or more OTU tables | |
| otutab_norm | Normalize OTU table counts to same number of reads per sample | |
| otutab_otu_subset | Extract subset of OTUs | |
| otutab_sample_subset | Extract subset of samples | |
| otutab_sortotus | Sort OTUs by decreasing frequency | |
| otutab_stats | Report summary statistics for OTU table | |
| otutab_subsample | Subsample (rarefy) OTU table | |
| otutab_trim | Delete low-abundance counts, samples and OTUs | |
| pairs_global | Make pair-wise global alignments | |
| pairs_local | Make pair-wise local alignments | |
| qiimemap2otutab | Convert QIIME map file to classic format | |
| sam_filter | Convert SAM alignments to BLAST6 or human-readable format | |
| search_16s | Find 16S genes in chromosomes or contigs | |
| 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 | |
| sinaps | Predict attributes (traits) from OTU sequences | |
| sintax | Predict taxonomy | |
| sortbylength | Sort by decresing sequence length | |
| sortbysize | Sort by decresing abundance (size= annotations) | |
| tree2distmx | Generate distance matrix from tree | |
| tree_cvt | Convert between Newick and tabbed formats | |
| ublast | Fast database search (local alignment similar to BLAST) | |
| uchime2_ref | Find chimeras by database search | |
| uchime3_denovo | Filter chimeras in denoised amplicon sequences | |
| udb2bitvec | Create bit vector index for search_16s | |
| udb2fasta | Extract sequences from UDB file | |
| udbinfo | Report index parameters used to make UDB file | |
| unbias | Correct for abundance bias in OTU table | |
| uncross | Detect cross-talk from OTU table | |
| unoise3 | Correct errors (denoise) amplicon reads, includes chimera filter | |
| uparse_ref | Classify mock community sequences (recognizes chimeras and read errors) | |
| usearch_global | Fast database search (indexed, global alignment) | |
| usearch_local | Fast database search (indexed, local alignment) |