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Difference between revisions of "Interactive mode"

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When you start mothur, you will see a screen that looks like this:
 
When you start mothur, you will see a screen that looks like this:
  
mothur v.1.5.0
+
mothur v.1.5.0
Last updated: 9/6/2009
+
Last updated: 9/6/2009
  
by
+
by
Patrick D. Schloss
+
Patrick D. Schloss
  
Department of Microbiology & Immunology
+
Department of Microbiology & Immunology
University of Michigan
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University of Michigan
pschloss@umich.edu
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pschloss@umich.edu
http://www.mothur.org
+
http://www.mothur.org
  
  
Distributed under the GNU General Public License
+
Distributed under the GNU General Public License
  
Type 'help()' for information on the commands that are available
+
Type 'help()' for information on the commands that are available
  
Type 'quit()' to exit program
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Type 'quit()' to exit program
  
mothur >  
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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:
 
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:

Revision as of 12:33, 29 September 2009

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
pschloss@umich.edu
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
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()

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.