cbrc
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!

Source

Download

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 7.221.

Installation (as root)

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!! There was a compatibility problem with gcc version 4.8.  This problem has been fixed in version 7.154 (2014/May).

Installation (as a non-root user)

See here.