If you are looking for programs to cluster sequences, a paper published in Briefings in Bioinformatics in July describes several options. Although it is motivated by metagenomics, the programs are generally useful for all other genomics problems.
Sequence clustering is not a new topic; it existed long before the emerging of metagenomics and NGS technologies. In the past, many available clustering programs were used for clustering protein sequences such as ProtoMap , ProtoNet , RSDB , GeneRAGE , TribeMCL , ProClust , UniqueProt , OrthMCL , MC-UPGMA , Blastclust  and CD-HIT . Many methods were also used for clustering expressed sequence tags (ESTs), such as Unigene , TIGR Gene Indices , d2_cluster  and several others .
Many of the above clustering methods require all against all comparisons of sequences for optimal results, so they are very computational intensive for large data sets. A method for reducing the intensive requirement arose with CD-HIT. Thus, with the rapid growth of sequence data, the fast program CD-HIT become a very popular clustering tool; it has been widely used in many areas such as preparing NR reference databases . CD-HIT uses a greedy incremental algorithm. Basically, sequences are first ordered by decreasing length, and the longest one becomes the seed of the first cluster. Then, each remaining sequence is compared with existing seeds. If the similarity with any seed meets a pre-defined cutoff, it is grouped into that cluster; otherwise, it becomes the seed of a new cluster. More recently, several new fast programs, including Uclust , DNACLUST  and SEED , have been developed using greedy incremental approaches similar to that introduced by CD-HIT. These methods use various heuristics and achieved high speed in clustering NGS sequences. Herein, we briefly introduce the features and functions of these programs.