cbrc
MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

This server is in the process of switching from HTTP to HTTPS.  No change is necessary for links, bookmarks, etc. in most cases, as they are redirected to HTTPS. 

However, if you are automatically downloading packages (.zip, .tgz, etc) using cURL or other tools, please change the URL from:
http://mafft.cbrc.jp/...
to:
https://mafft.cbrc.jp/...

See here for detailed information.

All-in-one package for Windows

Download

Multithreading is experimentally supported (2014/Sep).

Installation

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

It is better not to use parentheses in the destination folder name, like C:\somewhere\mafft-7-win64(1).

Usage

  1. Copy an input file (fasta format; example) into the mafft-win folder (extracted from the package).
  2. Double-click on mafft.bat.  Windows SmartScreen may warn that this app is not signed.

    To run the signed version, right-click (not double-click) on mafft-signed.ps1 and select Run with PowerShellConfirm that Publisher is "Osaka University".

  3. Follow the prompts.  Filename extension (eg., .txt) must be typed, if any.

    cui

Notes