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Interactive mode

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Revision as of 12:37, 29 September 2009 by Westcott (Talk | contribs) (Reverted edits by Westcott (Talk) to last version by Pschloss)

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

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

Patrick D. Schloss

Department of Microbiology
The University of Massachusetts

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.