New features and changes in USEARCH v4
| Feature | Version |
| Uchime option --[no]chimetopctl. If enabled, the top hit is used as a control. This means that a chimera model is rejected if it has identity <= the top database hit. This may be a useful check if the reference database is free of chimeras, but in de novo mode this may suppress good hits because there may be families of closely related chimeric sequences. Default is --chimetopctl. | 4.0.41 |
| Improved UCHIME algorithm with de novo mode. | 4.1.93 |
| --[no[chimetopctl option no longer supported. | 4.1.93 |
| --maxtargets option is no longer supported. | 4.2.1 |
| --sortsize and --minsize options for cluster size. | 4.2.1 |
| --slots option for compressed indexes. | 4.2.1 |
| --chimeras filename and --nonchimeras filename options added to --uchime. | 4.2.66 |
| --derep_fullseq, --derep_subset and --bithash options for exact dereplication. | 4.2.66 |
| --consout filename option for consensus sequences. | 4.2.66 |