This is the source code for the RNAstructure program 'partition' which 
calculates the thermodynamic energy partition function for an RNA or DNA 
sequence, and can be used to predict base-pairing probabilities.

This code is released under the MIT licence. See "MIT-license.txt" for details.

This program is part of the RNAstructure software package, which includes 
additional tools for RNA secondary structure prediction and analysis.
The full package is freely available under the GNU GENERAL PUBLIC LICENSE (GPL)
Version 2 and can be obtained from the Mathews lab website,
http://rna.urmc.rochester.edu.

### Specifying the location of Thermodynamic Parameter files (DATAPATH)
RNAstructure uses a set of nearest neighbor thermodynamic parameters, which are 
read from files in a user-configurable directory. An environment variable, 
DATAPATH needs to be set to indicate the location of this directory.
The default location is RNAstructure/data_tables/
See the following page for more information:
https://rna.urmc.rochester.edu/Text/Thermodynamics.html

Help for the partition program can be found online at:    
https://rna.urmc.rochester.edu/Text/partition.html

Please contact David Mathews with any question or comments:
David_Mathews@urmc.rochester.edu
