Disclaimer

• March 21st, 2009, version 2.0 was released.
• This is the version used in Mirela Andronescu's PhD thesis and subsequent papers from this thesis.
• Completed functions on parameter estimation for extended models (for Chapter 6 of Andronescu's PhD thesis).
• NOTE: Since a lot of variables use the stack, you might get "Segmentation fault" when you try to run simple commands, particularly when you use suboptimals. If you get that, you can edit the file "include/constants.h" and set the constants MAXSUBSTR and/or MAXSLEN to a lower value. In a future version, I might reimplement parts of the code to use the heap instead of the stack, but I can't promise it.
• July 2nd, 2008, version 1.11 was released.
• Added a few more options to the simfold and pairfold interfaces.
• Started functions on parameter estimation of an extended model.
• February 29th, 2008, version 1.10 was released.
• Added a few new functions in src/common/params.cpp, that compute the energy and parameter counts for some restricted cases, to be used by pseudoknotted prediction programs.
• Added a new driver, called test_get_features.cpp, that uses the new functions.
• October 19th, 2007, version 1.9 was released.
• Fixed a small bug in the file s_specific_functions.cpp, in the function simfold_ordered_suboptimals. This may have affected the energy values of suboptimal structures for simfold, which were computed without the dangling ends. Now the correct energy model is used, which includes the dangling ends.
  
• August 6th, 2007, version 1.8 was released.
• Fixed a stupid little bug in simfold.cpp, which gave wrong values when folding DNA at any temperature, or RNA at temperatures other than 37C.
  
• July 2nd, 2007, version 1.7 was released.
• Completed and optimized the partition function calculation for simfold. It also include base pair probability and gradient computations, for the cases when dangling end energy values are completely ignored (reasonably fast), and for the case where dangling ends are included in a way consistent with the original model, except that the 3' dangling ends are always assumed to be smaller than the 5' correcponding ones. This is hairy and slower.
  
• Added a new driver: simfold_pf, which shows how you can compute the partition function and base pair probabilities.
  
• June 18th, 2007, version 1.6 was released.
• Added the ISMB 2007 thermodynamic parameters. NOTE! We are working hard on improving the quality of the energy parameters, so use them with caution! New parameters to come soon!
• Fixed a few more bugs in the recurrences for simfold_restricted. It should be bug free now as far as I know.
  
• Made the code compatible with Linux SUSE 10.1 systems.
• Added a few more options to the simfold driver.
• The partition function calculation and base pair probabilities is functional now, but still under heavy testing.
  
• November 15th, 2006, version 1.5 was released.
  
• Fixed a bug in simfold_restricted: it was not working correctly when we had a restricted 0 size hairpin: ().
• Added better comments to simfold.
• Fixed a little bug which made some hairpin loops not consider the tri and tetra loop bonuses, if the input sequence was in lowercase.
• Started partition function calculation for simfold - not finished yet.
  
• November 1st, 2005, version 1.4 was released.
• added the function pairfold_mfe_nointra, which computes only intermolecular interactions, and no intramolecular interactions. This may be useful for some applications, and it's order (len(seq1) len(seq2)).
  
• September 27th, 2005, version 1.3 was released.
• fixed a little bug in the script get_code.csh, which wasn't copying all header files correctly
• added a section on Installation in the README file
• fixed a bug in the file params.cpp which plays with the parameters - didn't affect any of the current binaries.
  
• June 23rd, 2005, version 1.2 was released.
• solved two more memory leaks that made pairfold with suboptimals crash;
• added the restricted version for SimFold.
  
• Apr 17th, 2005, version 1.1 was released.
• several memory leaks have been solved.
  
• Feb 21st, 2005, version 1.0.3 was released.
• created Windows DLL version;
• updated entropy and enthalpy parameters with the values from Santalucia 2004, for the function to compute melting temperature directly from parameters;
  
• renamed this Tm function with a more meaningful name;
• the "params/" directory is now more flexible, it can be located in any place, and the path relative to the executable has to be specified in the driver.
  
• Feb 6th, 2005, version 1.0.2 was released.
  
• added a function to compute entropy and enthalpy for perfectly complementary pairs, directly from parameters;
  
• added a new melting temperature function, to use the above entropy and enthalpy;
• fixed a bug in the melting temperature for non-self-complementary sequences with different concentrations;
• insert an automatic detection of self-complementarity, which assumes a sequence is self-complementary if it has an even number of bases and if the first half is the perfect reverse complement of the second half;
• added a new driver called melting_temp.cpp, to deal with melting temperatures. A good input file is a file which lists a set of probes from a paper by Owczarzy 2004 (one probe per line).
  
• Jan 29th, 2005, version 1.0.1 was released. For version 1.0.1, I applied very small modifications, to make the package compile and run on Windows (I used Visual C++ 6.0 on Windows 2K).
• Jan 21st, 2005, version 1.0 was released.
  

• dir params/ contains the thermodynamic parameters: Turner's parameters for RNA and Mathews' parameters for DNA. Usually you don't need to touch this.
  
• (NOTE: the DNA parameters in this package are different from the DNA parameters in the online version, so you will probably get (slightly) different results. Those are SantaLucia parameters and are not freely available).
  
• params/CG_best_parameters_ISMB2007.txt includes the parameters obtained in the ISMB 2007 paper.
• params/turner_partypes_fm363.txt includes the features used in the ISMB 2007 paper.
• params/turner_parameters_fm363_constrdangles.txt includes the Turner99 parameters for the same features, where two dangling end parameters have been slightly modified to obey the rule: 3' dangling end parameters are always <= the 5' dangling end parameters.
  
• dir include/ contains a few header files which need to be included in the drivers
• dir src/ contains the source codes
  
• dir CVS/ is the cvs default directory and contains version information. Don't remove it.
  
• simfold.cpp - a driver for SimFold only, minimum free energy computation
• simfold_pf.cpp - a driver for SimFold partition function and base pair probabilities
  
• pairfold.cpp - a rudimentary driver for PairFold only
• multifold.cpp - a rudimentary driver for MultiFold only
• multirnafold.cpp - a rudimentary driver for all SimFold, PairFold and MultiFold
• melting_temp.cpp - a driver to test function for melting temperature calculations of perfectly complementary strands
  
• test_get_counts.cpp - a driver to test functions that compute the free energy and parameter counts
  
• Makefile (valid only for Linux) - run make to compile all sources and all drivers. A static library called libMultiRNAFold.a is created, which contains all three pieces of software. If you want to compile only SimFold, run make -f Makefile_simfold. libsimfold.a will be created, and only teh simfold driver will be compiled. Same for the other two.
• get_code.csh is a csh script which allows you to get only one of the three pieces of software, in case you are not interested in the other two. Run it without arguments to see the usage message.