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File debian.changelog of Package TfReg

tfreg (4.0) stable; urgency=low

  * New parameters for DNA/RNA hybrids. 
  * Bug fixes. 
  * Documentation updates.

 -- Gerald Weber <gweberbh@gmail.com>  Fri, 21 Sep 2018 12:00:00 -0300

 tfreg (3.2) stable; urgency=low

  * New parameters for Cy3/Cy5-DNA. 
  * Fixed bug regarding average opening calculation which in certain circumstances would use periodic boundary conditions. 
  * Documentation updates.

 -- Gerald Weber <gweberbh@gmail.com>  Thu, 13 Jul 2017 12:00:00 -0300

tfreg (3.1) stable; urgency=low

  * New parameter files for group I RNA bulges.

 -- Gerald Weber <gweberbh@gmail.com>  Tue, 11 Apr 2017 12:00:00 -0300

tfreg (3.0) stable; urgency=low

  * Fixed important bug concerning matrix multiplications which affects the average opening profiles, especially for symmetric sequences. This may also affect, although very slightly, the melting index and predicted temperatures. Differences in both cases are around 0.01 or less compared to previous versions of tfreg.
  * Fixed bug from version 2.0 which was generating empty files for option -res=prediction with single sequences.
  * Added new base pair representation of type XY^z which introduces context-dependent base pairs.
  * Added optimized parameters for RNA GU. Linking to the library libboost_regex is now required.
  * Code clean up, removed gbc_exp from C++ name space.
  * Adding version identification, see first printed line when running tfreg.
  * You can now add easily your own model potentials.
  * Example scripts were revised for consistency, in particular they no longer accept the data folder as argument. Alternative data folders should be provided by setting the PREFIX command line variable.
 -- Gerald Weber <gweberbh@gmail.com>  Fri, 22 Jan 2016 12:00:00 -0300

tfreg (2.0) stable; urgency=low
  * Corrected harmless bug which was causing the last line of a parameter to be read twice. 
  * Added a new model -model=mes. 
  * Added new option -res=nncheck. 
  * Added optimized parameters for deoxyinosine. 
  * Files with extension .ver now have an additional column providing RMS(Delta T).

 -- Gerald Weber <gweberbh@gmail.com>  Wed, 17 Dec 2014 12:00:00 -0300

tfreg (1.2) stable; urgency=low

  * Corrected bug which would fail to predict temperatures with -pm=-1 from
    reg files also generated with -pm=-1.
 -- Gerald Weber <gweberbh@gmail.com>  Wed, 20 Nov 2013 17:00:00 -0300

tfreg (1.1) stable; urgency=low

  * Improved user documentation. 
  * New script tfreg-salt-regression.pl to generate regression files for 
    different salt concentrations. 
  * Corrected bug which caused the unnecessary recalculation of quadrature 
    weights, as a result TfReg now runs much faster.

 -- Gerald Weber <gweberbh@gmail.com>  Wed, 06 Feb 2013 14:31:09 -0300

tfreg (1.0) stable; urgency=low

  * Initial Release

 -- Gerald Weber <gweberbh@gmail.com>  Tue, 13 Nov 2012 18:04:24 -0300