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Command line mode

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In the command line mode you can run mothur directly from the terminal. This may be advantageous for people generating shell script pipelines. Following the name of the executable (i.e. mothur) you would type out the commands within quote marks and the first character being a pound sign (i.e. '#'). The commands should be separated by semicolons. For example, if you want to run the traditional analysis performed by dotur using the AmazonData.zip data set, then your command line should look like this:

escriba:AmazonData pschloss$ mothur "#read.dist(phylip=98_sq_phylip_amazon.dist, cutoff=0.1); cluster(); collect.single(); rarefaction.single()"

A related option is to run mothur in batch mode.