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!! The RNA structural alignment feature is incompatible with gcc 4.8.x.  Even if compilation succeeds, the result can be incorrect.  If you have this version of gcc only, use pre-compiled package (2014/Jan)

Installation (as a non-root user)

See here.