RIMD, Osaka Univ. Osaka Univ.
MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

All-in-one package for Windows



  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.


1 Copy an input file (fasta format; example) into the mafft-win folder, which was extracted from the package.
2 Double-click on baticon 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 ps1icon 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.