Multiple alignment program for amino acid or nucleotide sequences

Cygwin version

Installation

1. Install Cygwin. http://www.cygwin.com/
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.
2. Start Cygwin (Start → All Programs → Cygwin → Cygwin Bash Shell).

   

3. 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).

   

4. Save one of the .tar packages as a file.
• mafft-7.505-mingw64-signed.tar (64-bit, 2021/Jul)
• mafft-7.427-mingw32-signed.tar (32-bit, Not tested, DASH is unavailable, 2019/Mar/24)

Note:

• Cygwin version may be very slow if real-time scanning is performed by anti-virus software such as McAfee.  To avoid this problem, try Ubuntu version.
• .exe files in this package are signed.  Publisher is “Osaka University”.
• If you notice any problems, let us know (2016/Aug/11).
5. Copy or move the package into the Explorer window.
6. At the Cygwin window, type

   $ tar xfv mafft-7.505-mingw64-signed.tar -C /   
   

   Replace -mingw64- with -mingw32- if you downloaded the 32-bit version.

   

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.