New features and changes in USEARCH v5
| Feature | Version |
| Added support for UDB index files. This index file format supports very fast sensitive protein searches, both untranslated (similar to BLASTP) and translated (similar to BLASTX). | 5.0 |
| Changed --orfstyle default from 7 to 5. | 5.1 |
| Removed --strand and --frame options. | 5.1 |
| Improved smoothed identity method for identifying the top two candidate parents in UCHIME in cases with long terminal gaps due to varying length reference sequences.. Has no significant effect on benchmark results, but improves results on some real test data. | 5.1 |
| Changed --qmask and --dbmask options from obscure numbers to self-explanatory strings. Valid values are now seg, dust, default, user and upper. | 5.1 |
| Added --threads option. In v5.1, supported for searches using UDB indexes only. Will be extended to other commands in future versions. | 5.1 |
| Improved UDB and WDB index load times, substantially faster compared to v5.0. | 5.1 |
| Improved UDB indexing typically gives a ~2x speed improvement over v5.0. | 5.1 |
| Changed UDB file format to remove limit on database size. The --splitdb command is no longer needed or supported. The new format is not compatible with v5.0, so index files must be rebuilt using --makeudb. | 5.1 |