kClust: fast and sensitive clustering of large protein sequence databases

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Ultra-fast sequence clustering from similarity networks with SiLiX

(2011) Vincent Miele et al.   BMC BIOINFORMATICS

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree

(2011) N. Rappoport et al.   NUCLEIC ACIDS RESEARCH

Sequencing delivers diminishing returns for homology detection: implications for mapping the protein universe

(2010) Daniel Chubb et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE