execution of mothur is done from a command line. Because this is not a commercial piece of software, but rather software designed for microbial ecologists, by microbial ecologists, it is missing a few bells and whistles. Namely, the program is driven from the command line. This was a necessary design choice in order to serve researchers who like to use linux, mac, and windows operating systems.

Starting mothur


To run mothur on a Mac, you need to open the Terminal program. If it isn’t already on your dock, in the Finder press Command-Shift-A, which will open a window with the list of programs on your machine. From there open the Utilities folder. Drag the Terminal.app icon to your doc and click on the icon to open the terminal window. Alternatively, you can double click on the Terminal.app icon in the Utilities folder without moving it to your dock. The terminal window automatically opens in your home directory (/Users/yourname/ aka ~/). You should see something like:

escriba:~ pschloss$ 

Note that throughout the wiki, we’ll represent that with a simple prompt:

You next need to move to the folder containing your data. If you decompress the amazondata.zip file into a folder in your home directory, you can move there by typing:

$ cd AmazonData

If you type:

$ ls

You will see the contents of the AmazonData folder.

Now you need to know the path of the mothur executable. Assuming you installed mothur to a folder called mothur in your home directory, type:

$  ../mothur/mothur


$  ~/mothur/mothur

If you’re a unix pro, you can add mothur to your path so that you only need to type:

$ mothur

This will put mothur into an interactive mode. Alternatively, to put it into a batch mode where you provide a file of commands you need to type:

$  ~/mothur/mothur batchfile


download file

Installation from the command line:

 mkdir mothur
 cd mothur
 unzip ../Mothur.source.zip

running mothur, from the command line:

 cd mothur


mothur is a command line program. You can run it in interactive mode by double-clicking on the mothur.exe executable.

Alternatively, you can run it from the command line. To open a terminal in windows select Run from the Start menu. Type cmd into the run window and click OK. This will bring up a terminal window. From here, it is convenient to move to the directory containing your data so it can be access without specifying path names within mothur. If you decompress the amazondata.zip file into a folder in your My Documents directory, you can move there by typing:

cd "C:\Documents and Settings\`<your name>`\My Documents\AmazonData"

Now you need to know the path of the mothur executable. Assuming you placed mothur in a folder called mothur on your C drive, you can start mothur in interactive mode by typing:


The following error will be reported when starting mothur, but can be safely ignored:

'clear' is not recognized as an internal or external command, operable program or batch file.

You can also run mothur in batch mode. In batch mode, commands from a file will be processed. To run mothur in batch mode give it the name of the file containing the commands you wish to have executed:

 C:\mothur\mothur.exe C:\mothur\commands.txt

If you wish to avoid the use of the command line, you can also run mothur in batch mode by creating a batch file. For example, create a file called mothur.bat in the directory containing mothur.exe. Edit this batch file to contain the lines:

mothur commands.txt

You can now double click on mothur.bat to execute mothur in batch mode with the commands given in commands.txt. The pause line causes the command line window that open to remain open until you press a key. This will allow you to inspect your results.

Available modes

Most users will prefer to run mothur from the default interactive mode. If you are developing a pipeline that includes mothur, a command line mode and batch mode are available as well.