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Batch mode

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In batch mode you can supply a file with a list of commands that you want mothur to run. This would be useful if you have a set of analyses that you know you are going to run and don't want to have to wait for them to run. For example, if you want to run the traditional analysis performed by dotur using the AmazonData.zip data set, then your batch file should look like this:

cluster(phylip=98_sq_phylip_amazon.dist, cutoff=0.1)
collect.single()
rarefaction.single() 

To run mothur in batch mode enter the name of the batch file after the program name. For example:

escriba:AmazonData pschloss$ ../mothur/mothur batchfile

If you want to enter any comments in the batch file, simply make sure that the first character on the line is a pound (i.e. #) character:

#This is a batch file for running the equivalent of dotur
cluster(phylip=98_sq_phylip_amazon.dist, cutoff=0.1)
collect.single()
rarefaction.single()

Of related interest is the command line mode.