Multiple alignment program for amino acid or nucleotide sequences

Experimental

How to install MAFFT to a non-default location

By default, MAFFT is installed to /usr/local/.  To change the installation location, modify Makefile as follows.

Also use this procedure when you do not have the root (administrator) account of the Linux (or UNIX) system.

1. Download the source package (mafft-x.xxxxxxxx-src.tgz).
2. Untar the source package.

   % tar xfvz mafft-x.xxx-with-extensions-src.tgz
   mafft-x.xxx-with-extensions/
   mafft-x.xxx-with-extensions/binaries/
   mafft-x.xxx-with-extensions/test/
   mafft-x.xxx-with-extensions/test/sample.dpparttree
   ...
   

3. Edit the first line of Makefile in the 'core' directory as follows.

   % cd mafft-x.xxx-with-extensions/core/
   % vi Makefile (any other text editor is ok.)
   
   From:
   PREFIX = /usr/local
   To:
   PREFIX = /home/your_home/somewhere (must be absolute path)
   

4. Also edit the third line of Makefile.

   From:
   BINDIR = $(PREFIX)/bin
   To:
   BINDIR = /home/your_home/bin (or elsewhere in your command-search path)
   

5. Compile and install.

   % make clean
   % make
   % make install
   

6. (Optional; Versions≥7.330 only) To enable MPI for a PC cluster, modify PREFIX in MPI/Makefile.

   Make sure that mpicc and mpirun, from the same library, work.
   
   % cd ../../
   % cd mafft-x.xxx-with-extensions/MPI/
   % vi Makefile (any other text editor is ok.)
   
   From:
   PREFIX = /usr/local
   To:
   PREFIX = /home/your_home/somewhere (must be absolute path)
   

   Ask administrator of your PC cluster where mpicc is.
7. (Optional) Compile and install the component for MPI.

   % make clean
   % make
   % make install
   

If you have downloaded the '-with-extension' package, make a modification to the 'extensions' directory.

If you had set the MAFFT_BINARIES variable at the previous installation, unset the variable.