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-6.717-with-extensions-src.tgz Beta 
  (supports RNA structural alignments as well as protein/DNA/RNA sequence aliginments; license notice)
• mafft-6.717-without-extensions-src.tgz Beta 
  (supports protein/DNA/RNA sequence alignments only; license notice)

Installation (as root)

% gunzip -cd mafft-x.x-src.tgz | tar xfv -
% cd mafft-x.x/core/
% make clean
% make
% su
# make install 

Programs are installed into /usr/local/bin/ and /usr/local/lib/mafft/ by default.  If you want to install them into different directories, see here.

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.