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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 than other clustering programs, for example BLASTCLUST. Therefore it can handle very large databases, like NR. The first version was released in 2001, the second version was publishes in 2002 with significant improvements. Since 2004 its hosted at as an open source project which helped to develop the program even more. Its still under active development and there will be new features and programs out in the future.

Installed Version

The following versions are installed and currently available...

... on environment hpc-env/8.3:

  • CD-HIT/4.8.1-GCC-8.3.0
  • CD-HIT/4.8.1-iccifort-2019b

... on environment hpc-uniol-env

  • CD-HIT/4.6.4

Using CD-HIT with the HPC Cluster

If you want to find out more about CD-HIT on the HPC Cluster, you can use the command

module spider cd-hit

This will show you basic informations e.g. a short description and the currently installed version.

To load the desired version of the module, use the command, e.g.

module load CD-HIT/4.6.4-foss-2016b-2015-0603

Always remember: this command is case sensitive!

After loading the module, you can run CD-HIT by using following command

cd-hit [Options]


The project page can be found here. Although, the most recent information can be found on github since the project moved there.