/cd-hit

This CD-HIT is a part of other programs.

Primary LanguageC++GNU General Public License v2.0GPL-2.0

For cd-hit

Module

This is the part of cd-hit modified by gitee@wym6912 / github@wym6912, which is a module of the other program. This module only have these parts in below:

cd-hit
cd-hit-est
cd-hit-454

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.

Compile cd-hit on MacOS

To install CD-HIT on MacOS, first install gcc on your system. To use Homebrew, 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 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.