Multiple alignment program for amino acid or nucleotide sequences

The pre-compiled packages (for Macintosh, for Windows) are much easier to install than this, unless you need MPI.

Source

Download

Latest version

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; Versions≥7.350 only) To enable MPI-parallelized version of G-INS-1, L-INS-1 and E-INS-1,

   Make sure that mpicc and mpirun, from the same library, work.
   
   % cd mafft-x.x/MPI/
   % make clean
   % make
   % su
   # make install
   

   Ask administrator of your PC cluster where mpicc is.
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
   

   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.

Usage

See here.