CD-HIT is a program for clustering DNA/protein sequence database at high identity with tolerance.

References:

• Clustering of highly homologous sequences to reduce the size of large protein database, Weizhong Li, Lukasz Jaroszewski & Adam Godzik, Bioinformatics, (2001) 17:282-283. PDF Pubmed

• Tolerating some redundancy significantly speeds up clustering of large protein databases, Weizhong Li, Lukasz Jaroszewski & Adam Godzik, Bioinformatics, (2002) 18:77-82. PDF Pubmed

• Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences, Weizhong Li & Adam Godzik, Bioinformatics, (2006) 22:1658-9. PDF Pubmed