CD-HIT-EST clusters a nucleotide dataset into clusters that meet a user-defined similarity threshold, usually a sequence identity. The input is a DNA/RNA dataset in fasta format and the output are two files: a fasta file of representative sequences and a text file of list of clusters. Since eukaryotic genes usually have long introns, which cause long gaps, it is difficult to make full-length alignments for these genes. So, CD-HIT-EST is good for non-intron containing sequences like EST.
Ying Huang, Beifang Niu, Ying Gao, Limin Fu and Weizhong Li. CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics, (2010). 26:680
CD-HIT was originally a protein clustering program. The main advantage of this program is its ultra-fast speed. It can be hundreds of times faster than other clustering programs, for example, BLASTCLUST. Therefore it can handle very large databases, like NR.
The 1st version of this program, CD-HI, was published and released in 2001. The 2nd version, called CD-HIT, was published in 2002 with significant improvements. Since 2004, CD-HIT has been hosted at bioinformatics.org as an open source project.
Since its release, CD-HIT has been getting more and more popular. It has a significant user base, I estimated at over several thousands users. It is used at many research and educational institutions. For example, at UniProt, CD-HIT is used to generate the UniRef reference data sets (http://www.pir.uniprot.org/database/DBDescription.shtml). It is also used in PDB to treat redundant sequences (http://rutgers.rcsb.org/pdb/redundancy.html).
In 2006, the 3rd major updates were published and released with abilities to perform various jobs like clustering a protein database, clustering a DNA/RNA database, comparing two databases (protein or DNA/RNA), generating protein families, and many others.
The CD-HIT web server was implemented in 2009, which allows users to cluster or compare sequences without using command CD-HIT. The server provides interactive interface and additional visualization tools. It also provides pre-calculated and regularly updated sequence clusters for several widely used databases.
CD-HIT-454, a special version of CD-HIT was implemented in 2010 to cluster artificial duplicated reads in pyrosequencing (454) data.
Currently, CD-HIT package has many programs: cd-hit, cd-hit-2d, cd-hit-est, cd-hit-est-2d, cd-hit-para, cd-hit-2d-para, psi-cd-hit, psi-cd-hit-2d, cd-hit-454. I also developed some utility tools, written in Perl, to help run and analyze CD-HIT jobs.
NOTE to installer:
The tool_dependency will set an environment variable: "CDHIT_SITE_OPTIONS" to -M 4000 -T 0 which will be in the commandline.
You can adjust the values of -M and -T to match the memory and thread capabilities of your site.