RIMD, Osaka Univ.

Osaka Univ.

MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

All-in-one package for Mac OS X

Recommended only when redistributing MAFFT within another program package.
Otherwise, try the standard package.

Download

mafft-7.490-mac.zip (Should run on OS X 10.?, macOS 10.12 – 11.4)
mafft-7.526-mac.zip (Should run on macOS 10.12 –) in Alpha testing

Installation

Open a Terminal window (Finder → Applications → Utilities → Terminal).

Unzip the package in any folder you like.

$ cd /somewhere/
$ unzip mafft-7.490-mac.zip

The mafft-mac folder is generated. This folder has the mafft.bat script and the mafftdir subfolder.
```
$ cd /somewhere/
$ ls -F
mafft-mac/
$ cd mafft-mac/
$ ls -F
mafft.bat*    mafftdir/
```
If you want to move the installation to another location, just move the entire mafft-mac folder to the new location.

Usage (Command-line mode)

Run the mafft.bat script with the full path.

% /somewhere/mafft-mac/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-mac/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.

Copy your input file to the mafft-mac folder,
```
% cp input.txt /somewhere/mafft-mac
```
Go to the mafft-mac folder,
```
% cd /somewhere/mafft-mac
```

Type ./mafft.bat and follow the prompts.

% ./mafft.bat

---------------------------------------------------------------------
   MAFFT v7.490 (2021/Oct/30)
        MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)
        https://mafft.cbrc.jp/alignment/software/
---------------------------------------------------------------------

Input file? (FASTA format; Folder=/somewhare/mafft-mac)
@ input.txt