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For cd-hit Requirements Since 4.8.1, cd-hit supports .gz format input file. This requires zlib library. zlib should be install in most Linux systems, so cd-hit should be compiled without issue. If your system don't have zlib, please install it first. * On Ubuntu, to install zlib: sudo apt install zlib1g-dev * On CentOS, to install zlib: sudo yum install zlib-devel How to compile 1. Compile with multi-threading support (default): make 2. Compile without multi-threading support (if you are on very old systems): make openmp=no 3. Compile without zlib (if you can not install zlib): make zlib=no Having problems to compile Please contact the author For cd-hit-auxtools cd cd-hit-auxtools make Compile cd-hit on MacOS To install CD-HIT on MacOS, first install gcc on your system. To use Homebrew (https://brew.sh/), see https://formulae.brew.sh/formula/gcc@6. 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 For psi-cd-hit please download BLAST+ (not legacy BLAST) and install the executables in your $PATH For more information, please visit http://cd-hit.org Most up-to-date documents are available at https://github.com/weizhongli/cdhit/wiki cd-hit is also available as web server, visit http://cd-hit.org for web server address.