Multiple alignment program for amino acid or nucleotide sequences

All-in-one package for Linux

Download

• mafft-7.526-linux.tgz (64-bit only)

Installation

1. Open a Terminal window.
2. Untar the .tgz file in any folder you like.

   $ cd /somewhere/
   $ tar xfvz mafft-7.526-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)

• Run the mafft.bat script with the full path and input file name.

  % /somewhere/mafft-linux64/mafft.bat input.txt > output.txt
  

• Aliases (mafft-linsi, etc) are not available.  Full options have to be given.  For example, to run mafft-linsi,

  % /somewhere/mafft-linux64/mafft.bat --localpair --maxiterate 100 input.txt > output.txt
  

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 v7.467 (2020/May/14)
           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