Two different versions of DREME are provided: dreme for Python 2.7 and dreme-py3 for Python 3.x. The random number generator has changed between Python 2.7 and Python 3.x, so results between the two versions may differ if you don't explicitly provide a control sequence file.

<primary sequence file>

The name of a file containing sequences in FASTA format. The sequences should all be approximately the same length.

DREME writes its output to files in a directory named dreme_out, which it creates if necessary. You can change the output directory using the -o or -oc options. The directory will contain:

• dreme.html - an HTML file that provides the results in an interactive, human-readable format
• dreme.txt - a plain-text file of the results
• dreme.xml - an XML file that provides the results in a format designed for machine processing
• NAMEnc_CONSENSUS.png - PNG image files containing sequence logos for each of the motifs found by DREME (where NAME is the motif name and CONSENSUS is the consensus sequence of the motif)
• NAMErc_CONSENSUS.png - PNG image files containing sequence logos for each of the motifs found by DREME (where NAME is the motif name and CONSENSUS is the reverse-complement consensus sequence of the motif)

Additionally DREME can output motif logos if the -png and/or -eps options are specified.

Option	Parameter	Description	Default Behavior
Input/Output
-p	primary sequence file	The name of a file containing the primary sequences in FASTA format.	Required argument.
-n	control sequence file	The name of a file containing the control sequences in FASTA format.	DREME will create a set of control sequences by shuffling the primary sequences while preserving dimer frequencies.
-png		Output motif logo images in portable network graphics (png) format. This format is useful for display on websites.	Images are not output in png format.
-eps		Output motif logo images in Encapsulated Postscript (eps) format. This format is useful for inclusion in publications as it is a vector graphics format and can be easily scaled.	Images are not output in eps format.
Alphabet
General
-norc		Search only the given primary sequences for motifs.	Search the given primary sequences and their reverse complements for motifs when the alphabet is complementable.
-g	ngen	Set the number of REs to generalize. Increasing ngen will make the search more through at some cost in speed.	DREME will generalize 100 REs.
-s	seed	Set the seed for the random number generator used to shuffle the sequences. When the -n option is given the control sequences will be used instead of shuffling.	The random number generator is initialized with a value of 1.
Stopping Conditions
-e	e	Stop searching for motifs when the next motif's E-value is > e.	Stop discovering motifs if the E-value threshold of 0.05 is exceeded.
-m	m	Stop searching for motifs when m motifs have been found.	There is no limit on the number of discovered motifs.
-t	t	Stop searching for motifs when t seconds have elapsed.	There is no limit on the time taken to discover motifs.
Set Core Motif Width
-mink	mink	Set the minimum width of the motif core.	A minimum core width of 3 is used.
-maxk	maxk	Set the maximum width of the motif core.	A maximum core width of 7 is used.
-k	k	Set the width of the motif core. This sets minimum width and maximum width to the same number.	The defaults for minimum and maximum width are used.
Miscellaneous
-desc	description	Include the text description in the HTML output.	No description in the HTML output.
-dfile	desc file	Include the first 500 characters of text from the file desc file in the HTML output.	No description in the HTML output.
Experimental (use at own risk)
-l		Print list of enrichment of all REs tested.