cbrc
MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

Windows version

The Cygwin eivironment is required.  cygwin-icon

Installation

  1. Install Cygwin. http://www.cygwin.com/
  2. The default settings are mostly ok.  If you use user-define guide tree, the merge option, etc, then add the Ruby package in the Cygwin installer.

  3. Start Cygwin (Start → All Programs → Cygwin → Cygwin Bash Shell).

    cygwin_ss

  4. Type the following command at the Cygwin window,
    $ explorer.exe . &
    
    to open an Explorer window on the current folder (C:\cygwin\home\username in many cases).

    explorer_ss

  5. Save one of the .tar packages as a file.
  6. Copy or move the package into the Explorer window.
  7. At the Cygwin window, type
    $ tar xfv mafft-7.312-mingwxx.tar -C /
    
    xx = 32 or 64
    Do not forget -C /

    cygwin_ss

Usage

  1. Open a Cygwin window (Start → All Programs → Cygwin → Cygwin Bash Shell).
  2. At the Cygwin window, type
    $ explorer.exe . &
    
    to open an Explorer window on the current folder.
  3. Copy an input file (fasta format; example) into the Explorer window.
  4. At the Cygwin window, type
    $ mafft input.txt > output.txt
    
  5. The output.txt file is in the Explorer window.