Today I posted uclust v2.1. For information on new features and fixes, see this page. It includes a new clustering method I call clumping, which is my name for clustering with the goal of identifying clusters (clumps) of pre-determined size. Members of a given clump should be more similar to each other than to members of other clumps. The motivation for clumping is to divide a set of sequences into pieces that are small enough for a given method to handle — say, multiple alignment or phylogenetic tree estimation.
Does anyone out there know of a term for this type of clustering? Please let me know!
There is also a chimera detection algorithm (UCHIME) that can find chimeras de novo in a set of unclassified and unaligned reads. This is a work in progress, but is working pretty well so I thought I’d make it available.