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Interactive mode

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

mothur v.1.5.0
Last updated: 9/6/2009
Patrick D. Schloss
Department of Microbiology & Immunology
University of Michigan

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 > 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)

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