Multiple alignment program for amino acid or nucleotide sequences

All-in-one package for Windows

Download

• mafft-7.526-win64-signed.zip (2024/May)
• May be very slow if real-time scanning is performed by anti-virus software such as McAfee.  To avoid this problem, consider using Ubuntu version on Windows.
• Let us know if you have any problems in running this package.

Installation

1. Copy the downloaded .zip file into a folder to install MAFFT. 

   Better to avoid the Desktop and Documents folders, because these folders may be protected by "Controlled folder access" in "Ransomware protection" in Windows Defender.

2. Right-click on the .zip file and select Extract All. 

   When using other tools for extracting, there are rare cases where LF in text files in this package is converted to CRLF.  Make sure to keep LF.

Usage

1	Copy an input file (fasta format; example) into the mafft-win folder, which was extracted from the package.
2	Double-click on mafft.bat.  As this file is not signed, Windows Defender SmartScreen may warn that this app is unrecognized.  Select “More info” to run anyway.  Tested on Windows 10, 8.1 and 7.
2′	Alternatively, to run the signed version, right-click (not double-click) on mafft-signed.ps1 and select Run with PowerShell.  Confirm that Publisher is “Osaka University” if asked.  Tested on Windows 10 and 8.1.
3	Follow the prompts.  Filename extension (eg., .txt) must be typed, if any.

• At the prompt  Additional arguments?, type --thread n to enable multithreading, where n it the number of cores to use.  If unsure, type --thread -1, by which the number of physical cores is automatically counted and all physical cores are used (versions ≥7.375).
• Other flags, such as  --adjustdirection and --memsavetree, can be added at this prompt.

Notes

• The mafft.bat script works as a command-line program when arguments are given on Command Prompt.

  C:\somewhere\mafft-win>mafft.bat --out output.txt --localpair input.txt   
  

  This function had a problem in version 7.407 (released 2018/Jul).  Fixed in version 7.409 (2018/Aug). 

  To run mafft-signed.ps1, the signed version, use Windows PowerShell.

  PS C:\somewhere\mafft-win> Set-ExecutionPolicy -Scope CurrentUser AllSigned   
  PS C:\somewhere\mafft-win> .\mafft-signed.ps1 --out output.txt --localpair input.txt   
  PS C:\somewhere\mafft-win> Set-ExecutionPolicy -Scope CurrentUser Restricted   
  

  ExecutionPolicy is configured before and after running mafft in this case.

• These scripts can be called by any GUI application (eg., Geneious) on Windows.  "call" or "cmd.exe /C" is necessary to call mafft.bat.

  call C:\somewhere\mafft-win\mafft.bat --localpair --out output.txt input.txt
  

  cmd.exe /C C:\somewhere\mafft-win\mafft.bat --localpair --out output.txt input.txt
  

  To call the signed script, mafft-signed.ps1,

  powershell.exe -ExecutionPolicy AllSigned C:\somewhere\mafft-win\mafft-signed.ps1 --localpair --out output.txt input.txt
  

  There are more efficient ways to directly call binary executables (.exe), instead of a script, in Windows environment.  Contact us if necessary.

• RNA structural alignment options (X-INS-i and Q-INS-i) are not supported.
• If you want to move the installation to another location, just move the entire mafft-win folder to the new location.
• License is GPL.  The sources are available here.  A part of MSYS is included.