MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

The pre-compiled packages (for Macintosh, for Windows) are much easier to install than this!



Latest version:

The latest version uses at most x2 memory space in comparison with previous versions.  If it stops due to memory shortage, try version 7.222.

Installation to /usr/local/ (root account is required)

This procedure requires root access, as programs are installed into /usr/local/bin/ and /usr/local/libexec/mafft/ by default.  If you want to install MAFFT without being root, see here.
  1. Untar the package.
    % gunzip -cd mafft-x.x-src.tgz | tar xfv -
    % cd mafft-x.x/core/
  2. Compilation and installation
    % make clean
    % make
    % su
    # make install
  3. (optional) To enable RNA structural alignment (X-INS-i and Q-INS-i),
    % cd mafft-x.x/extensions/
    % make clean
    % make
    % su
    # make install
    BUG!! The extensions part had a compatibility problem with gcc 6.1.1.  This problem was fixed in version 7.301 (2016/Aug).

Installation to a non-default location (root account is not required)

See here.