2. Installation

CD-HIT can be copied under the GNU General Public License version 2 (GPLv2).

Most CD-HIT programs were written in C++. Installing CD-HIT package is very simple:

• download current CD-HIT at https://github.com/weizhongli/cdhit/releases, for example cd-hit-v4.6.6-2016-0711.tar.gz
• unpack the file with " tar xvf cd-hit-v4.6.6-2016-0711.tar.gz --gunzip"
• change dir by "cd cd-hit-v4.6.6-2016-0711"
• compile the programs by "make" with multi-threading (default), or by "make openmp=no" without multi-threading (on old systems without OpenMP)
• cd cd-hit-auxtools
• compile cd-hit-auxtools by "make"

To install CD-HIT on MacOS, first install gcc on your system (to use Homebrew, see https://brewformulas.org/gcc). Then locate the path to your g++ executable, (e.g. /usr/local/Cellar/gcc/6.3.0_1/bin/g++-6, note: yours g++ path is likely to be different), then use command like this:

• make CC=/usr/local/Cellar/gcc/6.3.0_1/bin/g++-6

Thanks to Conda communities, cd-hit may also be installed through conda. See https://anaconda.org/bioconda/cd-hit.

• conda install -c bioconda cd-hit