cd-hit

CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. CD-HIT was originally developed by Dr. Weizhong Li. CD-HIT is currently maintained by Dr. Li's group at UCSD (http://weizhong-lab.ucsd.edu/).

CD-HIT is very fast and can handle extremely large databases. CD-HIT helps to significantly reduce the computational and manual efforts in many sequence analysis tasks and aids in understanding the data structure and correct the bias within a dataset.

The CD-HIT package has cd-hit, cd-hit-2d, cd-hit-est, cd-hit-est-2d, cd-hit-454, psi-cd-hit, cd-hit-otu, cd-hit-lap, cd-hit-dup and over a dozen scripts for various clustering needs.