UCLUST v3.0
 

UCLUST v3.0
A new version of UCLUST has been posted. This program implements the UBLAST, USEARCH, UCLUST, UHIRE and UCHIME algorithms for database search, clustering and chimeric sequence detection respectively.

See here for the change log with a summary of new features, bug reports and fixes.

See here for the updated manual.

UBLAST
The most significant new feature in UCLUST v3.0 is UBLAST. This is a local database search algorithm based on USEARCH, except that local alignments instead of global alignments are generated. In this initial implementation, which should be regarded as an experimental prototype, gapless high-scoring segment pairs (HSPs) are found using an algorithm similar to the original BLAST described in Altschul et al. (JMB, 1990). E-values are computed using Karlin-Altschul statistics. Compared with USEARCH, this method is more sensitive and has better discrimination for low-identity proteins, and is recommended for applications such as gene assignment of metagenomic ORFs. Currently, translated search (like BLASTX and TBLASTX) is not supported, but I'm working on it.

UCLUST v2.1
UCLUST is evolving rapidly -- maybe some of you haven't upgraded to 2.1 yet. If so, you should check the UCLUST v2.1 announcement to read about the new features in that version. 

Upgrading to v3.0
Users with paid licenses should already have received an upgrade. Non-commercial users can upgrade by using the download page.