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

• gitlab

• mafft-7.525-with-extensions-src.tgz
• mafft-7.490-with-extensions-src.tgz
  (supports RNA structural alignments as well as protein/DNA/RNA sequence aliginments; license notice)

• mafft-7.525-without-extensions-src.tgz
• mafft-7.490-without-extensions-src.tgz
  (supports protein/DNA/RNA sequence alignments only; license notice)

Versions 7.463 – 7.486 had a serious bug in the FFT-NS-i option; unnecessarily much memory was requested and the calculation sometimes failed.  This bug also affected the --auto option.  Please use 7.487 or higher.  (2021/Jul)

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.