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

• mafft-6.902-with-extensions-src.tgz Beta 
  (supports RNA structural alignments as well as protein/DNA/RNA sequence aliginments; license notice)
• mafft-6.902-without-extensions-src.tgz Beta 
  (supports protein/DNA/RNA sequence alignments only; license notice)

Installation (as root)

This procedure requires root access, as programs are installed into /usr/local/bin/ and /usr/local/lib/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; linux only) To enable multithreading, uncomment line 8 of Makefile.

   % vi Makefile (any other text editor is ok.)
   ENABLE_MULTITHREAD = -Denablemultithread
   #Uncomment this to enable multithreading (linux only)
   

3. Compilation and installation

   % 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 (as a non-root user)

See here.