NUPACK SOURCE CODE VERSION HISTORY
Copyright (c) 2010 Caltech. All rights reserved.

Version 1.0 (October 1, 2003):
Initial release, single-stranded partition function capabilities.

Version 2.0 (January 30, 2007):
Major reissue with multistranded partition function capabilities and
equilibrium concentration determination, complete documentation.

Version 2.1 (October 28, 2007):
  Bug fixes: 
    -degenerate flag functionality fixed.
    Prompts for user input when none specified fixed and improved.
    Printing of header comments fixed and improved.
  New functionality:
    -cutoff flag introduced for executables pairs, complexes, and 
      concentrations.

Version 2.1.1 (October 2, 2009):
  Bug fix:
    Adjusted Makefiles and fixed I/O to be compliant with new versions
    of gcc.

Version 3.0 (November 10, 2010):
  Bug fixes:
        * complex enumeration fixed for high strand-count cases.
        * symmetry calculation fixed for some cases.

  New functionality:
        * Nucleic acid sequence design via efficient ensemble defect optimization
        * Ensemble defect calculations
        * DNA salt corrections
        * Improved run times due to code optimization
        * Updated User Guide
     
