RNAstructure Help
partition

partition is used to calculate the partition function for a sequence, which can be used to predict base pair probabilities.

<seq file>	The name of a file containing an input sequence. Note that lowercase nucleotides are forced single-stranded in structure prediction.
<pfs file>	The name of a partition function save file to which output will be written.

-d, -D, --DNA	Specify that the sequence is DNA, and DNA parameters are to be used. Default is to use RNA parameters.
-h, -H, --help	Display the usage details message.

-c, -C, --constraint	Specify a constraints file to be applied. This can be used to include folding constraints. For partition, current supported constraints are force pairs, force a nucleotide to be single stranded, and force a nucleotide to be double stranded. Default is to have no constraints applied.
-md, -MD, --maxdistance	Specify a maximum pairing distance; that is, the maximum number of bases between the two nucleotides in a pair. Default is no restriction on the distance between pairs.
-sh, -SH, --SHAPE	Specify a SHAPE constraints file to be applied. These constraints specificially use SHAPE pseudoenergy constraints. Default is no SHAPE constraint file specified.
-si, -SI, --SHAPEintercept	Specify an intercept used with SHAPE constraints. Default is -0.8 kcal/mol.
-sm, -SM, --SHAPEslope	Specify a slope used with SHAPE constraints. Default is -2.6 kcal/mol.
-t, -T, --temperature	Specify the temperature at which calculation takes place in Kelvin. Default is 310.15 K, which is 37 degrees C.

Reuter, J.S. and Mathews, D.H.
"RNAstructure: software for RNA secondary structure prediction and analysis."
BMC Bioinformatics, 11:129. (2010).
Mathews, D.H.
"Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization."
RNA, 10:1178-1190. (2004).
McCaskill, J.S.
"The equilibrium partition function and base pair probabilities for RNA secondary structure."
Biopolymers, 29:1105-1119. (1990).