We will be offering mothur and R workshops throughout 2019. Learn more.
When you start mothur, you will see a screen that looks like this:
mothur v.1.5.0 Last updated: 9/6/2009
by Patrick D. Schloss
Department of Microbiology & Immunology University of Michigan firstname.lastname@example.org http://www.mothur.org
Distributed under the GNU General Public License
Type 'help()' for information on the commands that are available
Type 'quit()' to exit program
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 > read.dist(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)