RIMD, Osaka Univ. Osaka Univ.
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

BUG!! Versions 7.380–7.392 had a bug in the --add and --merge options. 
Versions 7.396–7.468 also had a bug in parsing input filename.
Please update to version 7.470 or higher.

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. (optional) To enable DASH, uncomment the following line in Makefile:
    DASH_CLIENT = dash_client
    
  3. Compile and install
    % make clean
    % make
    % su
    # make install
    
  4. (optional) To enable RNA structural alignment (X-INS-i and Q-INS-i),
    % cd mafft-x.x/extensions/
    % make clean
    % make
    % su
    # make install
    

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

See here.