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

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.