CD-HIT
Description
CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. It 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.
License
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of cdhit and load default version of cdhit as
module avail cdhit/ # list available modules module load cdhit # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail cdhit
and choose explicit version you want to use.
Documentation
Documentation is at http://weizhong-lab.ucsd.edu/cd-hit/ref.php .