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 or please read the cdhit-users-guide.pdf. 
Most up-to-date documents are available at http://weizhongli-lab.org/cd-hit/wiki/doku.php?id=cd-hit_user_guide.

cd-hit was originally hosted at Google Code, some of the old releases are still available from https://code.google.com/p/cdhit/.

cd-hit is also available as web server, visit http://cd-hit.org for web server address.
