We will be hosting mothur and R workshops throughout 2018. Learn more.
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 email@example.com 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()
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)