| 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_otus_utax | OTU clustering by taxonomy prediction (UTAX algorithm) | |
| cluster_smallmem | Greedy clustering (UCLUST algorithm) | |
| derep_fulllength | Find unique sequences and abundances (old name for fastx_uniques) | |
| fastx_uniques | Find unique sequences and abundances | |
| tree2clusters | Generate clusters from tree by identity cutoff |