MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

Ubuntu version   New! 2017/Dec

For Windows 10 Versions 1709 (2017/Oct), 1803 (2018/Apr), 1809 (2018/Oct) and later.  Check your Windows version.

Install Ubuntu on Windows (steps 1–3 below) and subsequently install MAFFT on Ubuntu (steps 4–6).

Installation of Ubuntu 

  1. Turn on “Windows Subsystem for Linux”.  Reboot the PC if requested.

  2. Install Ubuntu from Microsoft Store.  Takes several minutes and then asks you to set a username and a password, which will be used in step 5.

  3. Launch Ubuntu from Start menu.
    ubuntu terminal

    (If the above procedure fails, see Microsoft Docs.)

Installation of MAFFT

  1. On the Ubuntu window, run the following command to download MAFFT package.
    $ wget https://mafft.cbrc.jp/alignment/software/mafft_7.471-1_amd64.deb 
    To paste this command into the Ubuntu window, use right button of mouse.  If it does not work, enable QuickEdit Mode.

  2. Install the package by:
    $ sudo dpkg -i mafft_7.471-1_amd64.deb 
    [sudo] password for username: (Type the password that was set in step 2)

  3. Check location and version number of MAFFT.
    $ which mafft
    $ mafft --version
    v7.471 (2020/Jul/3)

Usage (interactive mode)

  1. Suppose input file, eg, input.txt, is placed in   C:\Users\yourname\DATA
    This folder can be accessed from Ubuntu as /mnt/c/Users/yourname/DATA

    In short,  C: on Windows = /mnt/c on Ubuntu. 

  2. On Ubuntu window, change directory, cd, to the folder where input.txt is.
    $ cd /mnt/c/Users/yourname/DATA

    To check if input.txt actually exists in this folder, use the ls command.

    $ ls

  3. Just type  mafft  to start a text-based interactive interface:
    $ mafft
    and follow the prompts to select input file, output file and options.
    ubuntu terminal
  4. The output file has UNIX-style line-endings.  If Windows style is preferable, then open the file with wordpadicon WordPad to convert it.

Usage (command-line mode)

Running MAFFT from outside of Ubuntu

Ruby (optional)