cbrc
MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

All-in-one package for Linux

Recommended only when redistributing MAFFT within another program package.
Otherwise, try RPM or source.

Download

Installation

  1. Open a Terminal window.
  2. Untar the .tgz file in any folder you like.
    $ cd /somewhere/
    $ tar xfvz mafft-7.407-linux.tgz
    
  3. The mafft-linux64 folder is generated, which has the mafft.bat script and the mafftdir subfolder.
    $ cd /somewhere/
    $ ls -F
    mafft-linux64/
    $ cd mafft-linux64/
    $ ls -F
    mafft.bat*       mafftdir/
    
  4. If you want to move the installation to another location, just move the entire mafft-linux64 folder (that contains both mafft.bat and mafftdir) to the new location. 

Usage (Command-line mode)

Usage (Interactive mode; Versions ≥7.407; 2018/Jul)

Try this only when the command-line mode is not useful.
  1. Copy your input file to the mafft-linux64 directory,
    % cp input.txt /somewhere/mafft-linux64
    

  2. Go to the mafft-linux64 directory,
    % cd /somewhere/mafft-linux64
    

  3. Type ./mafft.bat and follow the prompts.
    % ./mafft.bat
    
    ---------------------------------------------------------------------
       MAFFT v7.407 (2018/Jul/23)
            MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)
            https://mafft.cbrc.jp/alignment/software/
    ---------------------------------------------------------------------
    
    Input file? (FASTA format; Folder=/somewhare/mafft-linux64)
    @ input.txt