Flag [input]	Description
–help	Displays available flags with descriptions.
–ssRegion [.txt file]	Forces nucleotides in the user-supplied file SSREGION to be single stranded. See SuperFold readme for file format description.
–pkRegion [.txt file]	Models structure around pseudoknotted base pairs in the supplied PKREGION file. See SuperFold readme for file format description.
–np [int]	Sets the number of processors (NP) available to SuperFold. Default: 2.
–SHAPEslope [float]	SHAPE pseudo-free energy slope used for structure modeling. Value optimized in previous work19,20. Default: 1.8 kcal/mol.
–SHAPEintercept [float]	SHAPE pseudo-free energy slope used for structure modeling. Value optimized in previous work20. Default: – 0.6 kcal/mol.
–differentialFile [.txt file]	User-supplied differential SHAPE file calculated from NMIA-1M6. Refines ΔGSHAPE energy function21.
–differentialSlope [float]	Sets the pseudo free-energy slope for the differential SHAPE reactivity values. Default: 2.1 kcal/mol.
–trimInterior [int]	Number of nucleotides to trim from interior partition function and fold calculations. Default: 300.
–partitionWindowSize [int]	Length of the partition function window size. Default: 1200 nucleotides.
–partitionStepSize [int]	Spacing between partition function windows. Default: 100 nucleotides.
–foldWindowSize [int]	Length of the Fold window size. Default: 3000 nucleotides.
–foldStepSize [int]	Spacing between Fold windows. Default: 300 nucleotides.
–drawSS	Include secondary structure diagrams for expanded regions of low SHAPE and Shannon entropy using the Pseudoviewer58 web service.