MAFFT version 7
Multiple alignment program for amino acid or nucleotide sequences
All-in-one package for Windows
2016/Nov/1, Released version 7.306.
2016/Nov/2, Fixed a problem in redirecting progress info to a file.
2016/Nov/3, Updated the compiler.
2017/Mar/28, Fixed a bug in version 7.310.
Let us know if you have any problems in running this version.
This version uses at most x2 memory space in comparison with previous versions. If it stops due to memory shortage, try version 7.222.
is experimentally supported (2014/Sep).
Right-click on the downloaded package (.zip) and select Extract All.
Do not use parentheses in the destination folder name, like C:\somewhere\mafft-7-win10(1).
Copy an input file (fasta format; example) into the mafft-win folder (extracted from the package) where the mafft.bat file is.
Double-click the mafft.bat file.
Follow the prompts.
Filename extension (eg., .txt) must be typed, if any.
Cygwin is not required.
The mafft.bat script works as a command-line program when arguments are given.
C:\somewhere\mafft-win>mafft.bat --localpair input.txt > output.txt
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 Added on 2012/Dec/3
cmd.exe /C C:\somewhere\mafft-win\mafft.bat --localpair --out output.txt input.txt
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.