cbrc
MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

This server is in the process of switching from HTTP to HTTPS.  No change is necessary for links, bookmarks, etc. in most cases, as they are redirected to HTTPS. 

However, if you are automatically downloading packages (.zip, .tgz, etc) using cURL or other tools, please change the URL from:
http://mafft.cbrc.jp/...
to:
https://mafft.cbrc.jp/...

See here for detailed information.

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 7.222.

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.