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  <changelog author="&lt;gweberbh@gmail.com&gt; 1.0" date="1352548800">First Public Release</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 1.1" date="1360152000">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.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 2.0" date="1418817600">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).</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 3.0" date="1453464000">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.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 3.1" date="1491912000">New parameter files for group I RNA bulges.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 3.2" date="1499947200">New parameters for Cy3/Cy5-DNA. Fixed bug regarding average opening calculation which in certain circumstances would use periodic boundary conditions. Documentation updates.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 4.0" date="1537358400">New parameters for DNA/RNA hybrids. Bug fixes. Documentation updates.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 5.0" date="1582632000">New parameters for DNA/TNA hybrids, new features and bug fixes.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 5.1" date="1584014400">New parameters for DNA mismatches.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 5.2" date="1594641600">New parameters for DNA+LNA/DNA and DNA+LNA/RNA. New 3D model.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 5.3" date="1605614400">New RNA salt-dependent parameters, new sprediction options. Corrections and new example scripts.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 6.0" date="1617796800">New LNA and DNA-Mg2+ parameters. Corrections and new example scripts.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 7.0" date="1646049600">New parameters for metal mediated DNA.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 7.1" date="1662033600">New parameters DNA with Mg2+ and K+.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 8.0" date="1756728000">New parameters for DNA/DNA, DNA/RNA and RNA/RNA in PEG, and inosine in RNA.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 5.1" date="1762948800">New parameters for DNA/RNA mismatches.</changelog>
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  <version epoch="0" ver="8.1" rel="1.1.1"/>
  <changelog author="&lt;gweberbh@gmail.com&gt; 1.0" date="1352548800">First Public Release</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 1.1" date="1360152000">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.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 2.0" date="1418817600">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).</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 3.0" date="1453464000">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.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 3.1" date="1491912000">New parameter files for group I RNA bulges.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 3.2" date="1499947200">New parameters for Cy3/Cy5-DNA. Fixed bug regarding average opening calculation which in certain circumstances would use periodic boundary conditions. Documentation updates.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 4.0" date="1537358400">New parameters for DNA/RNA hybrids. Bug fixes. Documentation updates.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 5.0" date="1582632000">New parameters for DNA/TNA hybrids, new features and bug fixes.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 5.1" date="1584014400">New parameters for DNA mismatches.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 5.2" date="1594641600">New parameters for DNA+LNA/DNA and DNA+LNA/RNA. New 3D model.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 5.3" date="1605614400">New RNA salt-dependent parameters, new sprediction options. Corrections and new example scripts.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 6.0" date="1617796800">New LNA and DNA-Mg2+ parameters. Corrections and new example scripts.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 7.0" date="1646049600">New parameters for metal mediated DNA.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 7.1" date="1662033600">New parameters DNA with Mg2+ and K+.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 8.0" date="1756728000">New parameters for DNA/DNA, DNA/RNA and RNA/RNA in PEG, and inosine in RNA.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 5.1" date="1762948800">New parameters for DNA/RNA mismatches.</changelog>
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  <version epoch="0" ver="5.0" rel="2.1"/>
  <changelog author="&lt;gweberbh@gmail.com&gt; 1.0" date="1406289600">First Public Release</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 1.1" date="1449748800">Documentation updates. Code clean up, removed gbc_exp from C++ name space. Linking to the library libboost_regex is now required. Added optimized parameter files at different salt concentrations for D-OW04 datasets. Added new parameters from the literature. Correcting bug which was not generating complementary sequence when cseq was not given. You can now specify a list of Ct concentrations in option -ct.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 2.0" date="1503662400">Modifications for hybrid DNA-RNA sequences with specific naming scheme for parameters. Documentation updates and corrections. Corrected parameter files P-BS86.par and P-FR86.par for RNA. 
Several new parameters from the literature. Added new option nnpo for using NN parameters only.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 2.1" date="1538740800">New parameters for RNA with salt dependence. New option for performing numerous salt corrections.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 2.2" date="1553256000">New parameter files for hybrid DNA-RNA. New option to require log files to be written in gzip format (new option -zlog). Redesign of NN calculation taking advantage of pointers, CPU times reduce by a factor of 7 compared to previous versions. Added symmetry_correction_entropy to some parameter files. New parameter file P-SL04.par. boost_iostreams library is now required for compilation.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 3.0" date="1612180800">Extended data format.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 3.1" date="1629115200">New script files for RNA.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 4.0" date="1683633600">New parameters for LNA.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 4.1" date="1698321600">New parameters for DNA mismatches.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 5.0" date="1783512000">New parameters for 2-O-Methyl/RNA from literature.</changelog>
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  <version epoch="0" ver="5.0" rel="2.1"/>
  <changelog author="&lt;gweberbh@gmail.com&gt; 1.0" date="1406289600">First Public Release</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 1.1" date="1449748800">Documentation updates. Code clean up, removed gbc_exp from C++ name space. Linking to the library libboost_regex is now required. Added optimized parameter files at different salt concentrations for D-OW04 datasets. Added new parameters from the literature. Correcting bug which was not generating complementary sequence when cseq was not given. You can now specify a list of Ct concentrations in option -ct.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 2.0" date="1503662400">Modifications for hybrid DNA-RNA sequences with specific naming scheme for parameters. Documentation updates and corrections. Corrected parameter files P-BS86.par and P-FR86.par for RNA. 
Several new parameters from the literature. Added new option nnpo for using NN parameters only.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 2.1" date="1538740800">New parameters for RNA with salt dependence. New option for performing numerous salt corrections.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 2.2" date="1553256000">New parameter files for hybrid DNA-RNA. New option to require log files to be written in gzip format (new option -zlog). Redesign of NN calculation taking advantage of pointers, CPU times reduce by a factor of 7 compared to previous versions. Added symmetry_correction_entropy to some parameter files. New parameter file P-SL04.par. boost_iostreams library is now required for compilation.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 3.0" date="1612180800">Extended data format.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 3.1" date="1629115200">New script files for RNA.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 4.0" date="1683633600">New parameters for LNA.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 4.1" date="1698321600">New parameters for DNA mismatches.</changelog>
  <changelog author="&lt;gweberbh@gmail.com&gt; 5.0" date="1783512000">New parameters for 2-O-Methyl/RNA from literature.</changelog>
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