Multiple alignment program for amino acid or nucleotide sequences

New features in version 6.8

• Multithreading (linux only)
• A fast option to add sequence(s) to an existing alignment.

Download

• mafft-6.811-with-extensions-src.tgz Alpha 
  (supports RNA structural alignments as well as protein/DNA/RNA sequence aliginments; license notice)
• mafft-6.811-without-extensions-src.tgz Alpha 
  (supports protein/DNA/RNA sequence alignments only; license notice)

Edit Makefile

Mac and Windows → Nothing to do

Linux → To enable multithreading, uncomment line 8.

ENABLE_MULTITHREAD = -Denablemultithread
#Uncomment this to enable multithreading (linux only)

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.