For cd-hit 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 For cd-hit-auxtools cd cd-hit-auxtools make For psi-cd-hit please download legacy BLAST (not 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.