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set.dir allows you to redirect the output files created by mothur, or set the directory where mothur will look for input files. You can also set a default location for mothur to look if it can't find your files in the input location. This allows you to keep your reference files in one location.


mothur > set.dir(input=../inputFiles)
Changing input directory to /Users/Work/Desktop/inputFiles/


If output directory does not exist mothur will create it for you.

mothur > set.dir(output=../outputFiles)
Changing output directory to /Users/Work/Desktop/outputFiles/


By default tempdefault=mothur's executable location.

mothur > set.dir(tempdefault=../referenceFiles)
Changing default directory to /Users/Work/Desktop/referenceFiles/


The debug flag is used to indicate you want extra output to the screen and logfile. It will help you spot file format issues that cause mothur crashes.

mothur > set.dir(debug=t)

inputdir && outputdir

Mothur allows you to change the input and output directories globally in any command. For example:

mothur > summary.seqs(fasta=amazon.fasta, inputdir=../inputFiles)


Mothur allows you to set the location of the blast executables directory globally in any command. For example:

mothur > summary.seqs(fasta=amazon.fasta, blastdir=/usr/local/bin/blast)


The modifynames flag is used to indicate how you want mothur to treat sequence names containing ':' characters. Default=t, meaning if your sequence names contain ':' change them to '_' to avoid issues while making trees. modifynames=F will leave sequence names as they are.

Order of searching

When mothur is trying to find a file without a full path here are the order of searches.

1. Default path
2. Output directory
3. Input directory

The output directory is listed before the input directory because many of mothur's command create files that then are used as inputs on the next command.