We will be hosting mothur and R workshops throughout 2018. Learn more.

Interactive mode

From mothur
Jump to: navigation, search

When you start mothur, you will see a screen that looks like this:

mothur v1.0
Last updated: 1/29/2009

by
Patrick D. Schloss

Department of Microbiology
The University of Massachusetts
pschloss@micro.umass.edu
http://schloss.micro.umass.edu/mothur


Distributed under the GNU General Public License

Type 'help()' for information on the commands that are available

Type 'quit()' to exit program

mothur >

All of your commands will be entered from the mothur prompt. You can get a list of commands by typing help() at the prompt and you can get more specific help for each command by typing command_name(help) at the prompt. For example:

mothur > align.seqs(help)

Would give you the help file information for the read.dist() command.


If you want to quit mothur you simply enter:

mothur > quit()

or

mothur > quit

With the exception of quit, all commands require you to provide an open and close parentheses. If you supply any options there cannot be a space between the option, the '=', and the option setting. To separate options, use a comma. For example:

mothur > cluster(method=furthest, cutoff=0.10)


Alternatively, If you know what commands you will be running, you can use either the command line mode or batch mode.