refs/tags/v2.6.4 | v2.6.4 | 4a0e008 | This is version v2.6.4 | 25 September 2023, 18:09:05 UTC |
refs/tags/v2.6.3 | v2.6.3 | eb8f860 | This is release v2.6.3 | 20 July 2023, 08:05:20 UTC |
refs/tags/v2.6.2 | v2.6.2 | dab2277 | This is release v2.6.2 | 21 June 2023, 08:56:58 UTC |
refs/tags/v2.6.1 | v2.6.1 | ecb70c3 | This is version 2.6.1 | 12 June 2023, 10:10:43 UTC |
refs/tags/v2.6.0 | v2.6.0 | 75241dd | This is version 2.6.0 | 10 June 2023, 06:44:02 UTC |
refs/tags/v2.5.1 | v2.5.1 | 59e1ee6 | This is version 2.5.1 | 07 June 2022, 14:29:27 UTC |
refs/tags/v2.5.0 | v2.5.0 | f58f58a | This is version 2.5.0 | 11 November 2021, 08:12:29 UTC |
refs/tags/v2.4.9 | v2.4.9 | 97ffeb4 | This is version 2.4.9 | 12 July 2018, 08:59:11 UTC |
refs/tags/v2.4.8 | v2.4.8 | 1f64e87 | This is version 2.4.8 | 23 June 2018, 11:16:35 UTC |
refs/tags/v2.4.7 | v2.4.7 | a4057a9 | This is version 2.4.7 | 13 June 2018, 20:01:51 UTC |
refs/tags/v2.4.6 | v2.4.6 | 2e92b5a | This is version 2.4.6 | 19 April 2018, 11:53:55 UTC |
refs/tags/v2.4.5 | v2.4.5 | eaf09dc | This is version 2.4.5 | 17 April 2018, 16:41:22 UTC |
refs/tags/v2.4.4 | v2.4.4 | 140d3db | This is release v2.4.4 | 06 March 2018, 18:02:54 UTC |
refs/tags/v2.4.3 | v2.4.3 | a4584fb | This is version 2.4.3 | 14 November 2017, 11:50:15 UTC |
refs/tags/v2.4.2 | v2.4.2 | efd9062 | This is version 2.4.2 | 13 October 2017, 14:09:21 UTC |
refs/tags/v2.4.18 | v2.4.18 | d6fbaf2 | This is version 2.4.18 | 23 April 2021, 11:58:28 UTC |
refs/tags/v2.4.17 | v2.4.17 | 5d0cf4f | This is version 2.4.17 | 25 November 2020, 01:00:55 UTC |
refs/tags/v2.4.16 | v2.4.16 | ea2e71f | This is version 2.4.16 | 15 October 2020, 06:42:32 UTC |
refs/tags/v2.4.15 | v2.4.15 | 3803414 | This is version 2.4.15 | 20 August 2020, 09:37:16 UTC |
refs/tags/v2.4.14 | v2.4.14 | 0b8ca4c | This is version 2.4.14 | 14 August 2019, 12:27:27 UTC |
refs/tags/v2.4.13 | v2.4.13 | 8cd1c6e | This is version 2.4.13 | 31 May 2019, 14:55:48 UTC |
refs/tags/v2.4.12 | v2.4.12 | 9bdedd5 | This is version 2.4.12 | 17 April 2019, 10:34:57 UTC |
refs/tags/v2.4.11 | v2.4.11 | a82019f | This is version 2.4.11 | 18 December 2018, 17:13:08 UTC |
refs/tags/v2.4.10 | v2.4.10 | 11e29fc | This is version 2.4.10 | 27 September 2018, 13:20:08 UTC |
refs/tags/v2.4.1 | v2.4.1 | 4ebb155 | This is version 2.4.1 | 23 August 2017, 13:20:12 UTC |
refs/tags/v2.4.0 | v2.4.0 | feb0567 | This is version 2.4.0 | 01 August 2017, 19:55:15 UTC |
refs/tags/v2.3.5 | v2.3.5 | 16ad799 | This is version 2.3.5 | 14 April 2017, 07:13:34 UTC |
refs/tags/v2.3.4 | v2.3.4 | 23ff44f | This is version 2.3.4 | 10 March 2017, 13:33:22 UTC |
refs/tags/v2.3.3 | v2.3.3 | 2d14c2b | This is bugfix version 2.3.3 | 24 January 2017, 20:06:40 UTC |
refs/tags/v2.3.2 | v2.3.2 | a8f0e8d | This is release 2.3.2 | 18 January 2017, 14:38:33 UTC |
refs/tags/v2.3.1 | v2.3.1 | c6c3460 | This is version 2.3.1 | 15 November 2016, 10:02:58 UTC |
refs/tags/v2.3.0 | v2.3.0 | 61b4c41 | This is version 2.3.0 | 01 November 2016, 19:59:24 UTC |
refs/tags/v2.2.9 | v2.2.9 | 6d68832 | This is version 2.2.9 | 01 September 2016, 18:27:48 UTC |
refs/tags/v2.2.8 | v2.2.8 | f06beb2 | This is version 2.2.8 The following things have changed: Programs - Fix bad memory access in RNAalifold - Fix regression in RNAalifold to restore covariance contribution ratio determination for circular RNA alignments - Changed output of RNAsubopt in energy-band enumeration mode to print MFE and energy range in kcal/mol instead of 10cal/mol - Include latest Kinfold sources that make use of v3.0 API, therefore speeding up runtime substantially - Re-activate warnings in RNAeval when non-canonical base pairs are encountered Library - Fix syntactic incompatibilities that potentially prevented compilation with compilers other than gcc - Add function to compare nucleotides encoded in IUPAC format - Fix regression in energy evaluation for circular RNA sequences - Fix regression in suboptimal structure enumeration for circular RNAs - Allow for P i-j k-l commands in constraint definition files - Make free energy evaluation functions polymorphic - Add free energy evaluation functions that allow for specifying verbosity level - Secure functions in alphabet.c against NULL pointer arguments - Fix incompatibility with swig ≥ 3.0.9 - Fix memory leak in swig-generated scripting language interface(s) for user-provided target language soft-constraint callbacks - Expose additional functions to swig-generated scripting language interface(s) - Build Python3 interface by default - Start of more comprehensive scripting language interface documentation - Fix linking of python2/python3 interfaces when libpython is in non-standard directory Package - Restructured viennarna.spec for RPM based distributions - Several syntactic changes in the implementation to minimize compiler warnings - Fix --with-*/--without-* and --enable-*/--disable-* configure script behavior | 02 August 2016, 08:53:48 UTC |
refs/tags/v2.2.7 | v2.2.7 | ad760db | this is version 2.2.7 | 30 June 2016, 10:19:00 UTC |
refs/tags/v2.2.6 | v2.2.6 | e176a66 | This is version 2.2.6 | 21 June 2016, 11:51:21 UTC |
refs/tags/v2.2.5 | v2.2.5 | 6e23b18 | This is version 2.2.5 Changes to previous release: - Added Kinwalker as optional subproject - Added Python3 interface - Fixed regression in RNAcofold that prohibited output of concentration computations - Fixed behavior of RNAfold and RNAcofold when hard constraints create empty solution set (programs now abort with error message) - Added RNA::Params Perl 5 sub-package - Update RNA::Design Perl 5 sub-package - Simplified usage of v3.0 API with default options - Wrap more functions of v3.0 API in SWIG generated scripting language interfaces - Plugged some memory leaks in SWIG generated scripting language interfaces - Changed parameters of recursion status callback in vrna_fold_compound_t - Enable definition and binding of callback functions from SWIG target language - Added several configure options to ease building and packaging under MacOS X - Added new utility script RNAdesign.pl | 08 April 2016, 18:21:21 UTC |
refs/tags/v2.2.4 | v2.2.4 | 7c55e18 | This is version 2.2.4 Programs - Fixed bug in RNAsubopt that occasionally produced cofolded structures twice Library - Removed debugging output in preparations of consensus structure prediction datastructures | 18 February 2016, 13:54:27 UTC |
refs/tags/v2.2.3 | v2.2.3 | 735624b | This is version 2.2.3 Programs - Added postscipt annotations for found ligand motifs in RNAfold - Added more documentation for the constraints features in RNAfold and RNAalifold Library - Restore backward compatibility of get_alipf_arrays() | 08 February 2016, 18:45:35 UTC |
refs/tags/v2.2.2 | v2.2.2 | d1ff0af | This is version 2.2.2 Programs - Fix regression bug that occasionally prevented backtracking with RNAcofold --noLP | 08 February 2016, 17:21:42 UTC |
refs/tags/v2.2.10 | v2.2.10 | 8a0fb6a | This is version 2.2.10 - Mostly subopt bugfix | 06 September 2016, 13:26:51 UTC |
refs/tags/v2.2.1 | v2.2.1 | fcce317 | Version 2.2.1 Programs - Fix regression bug that made RNAcofold -a unusable - Fix regression bug that prohibited RNAfold to compute the MEA structure when G-Quadruplex support was switched on - Fix bug in Kinfold to enable loading energy parameters from file - Fix potential use of uninitialized value in RNApdist - Add manpage for ct2db Library - Fix MEA computation when G-Quadruplex support is activated Package - Allow for vendor installation of the perl interface using INSTALLDIRS=vendor at configure time - Install architecture dependent and independent files of the perl and python interface to their correct file system locations | 06 February 2016, 14:32:52 UTC |
refs/tags/v2.2.0b | v2.2.0b | ec2905f | Merge of constraints development branch on top of latest epars | 01 March 2014, 14:18:10 UTC |
refs/tags/v2.2.0-RC3 | v2.2.0-RC3 | 0b45f43 | Bump to Release Candidate 3 of ViennaRNA Package 2.2.0 | 04 May 2015, 13:42:26 UTC |
refs/tags/v2.2.0-RC2 | v2.2.0-RC2 | 9df7834 | Release Candidate 2 of ViennaRNA Package 2.2.0 | 04 May 2015, 13:15:38 UTC |
refs/tags/v2.2.0-RC1 | v2.2.0-RC1 | c16df79 | Pre-Release iversion for Dominiks SHAPE paper | 16 March 2015, 12:08:59 UTC |
refs/tags/v2.2.0 | v2.2.0 | 95779b1 | Version 2.2.0 Introduced new v3.0 API, hard + soft constraints, object oriented swig interface, LTO, libtool | 25 January 2016, 10:08:36 UTC |
refs/tags/v2.1.9 | v2.1.9 | ca58d48 | Version 2.1.9 This version fixes the dangling end / terminal mismatch contribution bug in the entire library. Therefore, computations might predict different structures/free energies if compared with version below 2.1.9! This is the actual changelog for v2.1.9: Progs: - Fixed integer underflow bug in RNALfold - Added Sequence Conservation index (SCI) option to RNAalifold Library: - Fixed bug in alifold partition function for circular RNAs - Fixed bug in alifold that scrambled backtracing with activated G-Quadruplex support - Fixed bug in alifold backtracking for larger G-Quadruplexes Utils: - Avoid warning for missing sequence constraint in switch.pl | 05 February 2015, 15:59:30 UTC |
refs/tags/v2.1.8 | v2.1.8 | dfbe0dc | Version 2.1.8: Progs: - Repaired RNAinverse user provided alphabet - Fix missing FASTA ID in RNAeval output Library: - prevent race condition in parallel calls of Lfold() - Fixed memory bug in Lfold() that occured using long sequences and activated G-Quad support Utils: - added latest switch.pl | 18 August 2014, 10:40:59 UTC |
refs/tags/v2.1.7 | v2.1.7 | f545b25 | This is version 2.1.7 Changes: - Python and Perl interface are compiling again under MacOSX - Fixed handling of C arrays in Python interface - fixed bug in RNALfold -z - added latest version of switch.pl - make relplot.pl work with RNAcofold output | 12 April 2014, 22:42:50 UTC |
refs/tags/v2.1.6 | v2.1.6 | 8c7bcb9 | This is version 2.1.6 Library: - updated moveset functions - final fix for discrepancy of tri-loop evaluation between partition function and mfe - pkg-config file now includes the OpenMP linker flag if necessary Programs: - New program ct2db allows for conversion of .ct files into dot-bracket notation (incl. pseudo-knot removal) - New commandline switches allow for elimination of non-canonical base pairs from constraint structures in RNAfold, RNAalifold and RNAsubopt | 27 January 2014, 09:54:54 UTC |
refs/tags/v2.1.5 | v2.1.5 | 7c331b1 | Final version of special hp equality between mfe and pf | 19 November 2013, 17:55:33 UTC |
refs/tags/v2.1.4 | v2.1.4 | fa00faf | v2.1.4: Library: - bugfix for gquad support in subopt() - bugfix for hexaloop evaluation in boltzmann factors Package: - new wininstaller files | 18 November 2013, 13:21:59 UTC |
refs/tags/v2.1.3 | v2.1.3 | 8d01df7 | Version 2.1.3 - fixed several g-quad related bugs - inserted base pair probability threshold parameter in RNAalifold - added g-quad support for RNAsubopt - Bugfix for ignored parameter files in RNAfold - Bugfix for RNAcofold segfault upon constraint folding without actually providing a constraint structure | 21 August 2013, 08:44:23 UTC |
refs/tags/v2.1.2 | v2.1.2 | 93e49c7 | - scripting interface stuff is now located in 'interfaces' directory - added python interface - added ArchLinux PKGBUILD file - prepared ruby interface (this is not ready for distribution yet) - added threadsafe variants for putoutpU_prob*() for LPfold - slight changes to the zuker_subopt and stochastic backtracking output of RNAsubopt - repaired g-quad support in RNAeval - fix of some memory leaks - fix for a reallocation bug in assign_plist_from_pr() - added windows installer scripts for NSIS | 24 May 2013, 13:03:49 UTC |
refs/tags/v2.1.1 | v2.1.1 | 4bc72a2 | backward compatibility bug fix for version 2.1.0 | 02 February 2013, 21:43:31 UTC |
refs/tags/v2.1.0 | v2.1.0 | 06198b6 | Version 2.1.0: Package: - The auxilary energy parameter files in the source tree now reside in the 'misc' directory. They are, however, still installed at the same locations as in previous versions of the Package. - To enable fast plotting of RNA2Dfold output we now also provide two gri-scripts "2Dlandscape_mfe.gri" and "2Dlandscape_pf.gri". To use them, simply redirect the output of RNA2Dfold into a text file and then call the appropriate script with the RNA2Dfold output filename as first parameter, e.g.: $ ./2Dlandscape_mfe.gri my_2Dfold_output.txt This will create a postscript file named "my_2Dfold_output.txt.ps" that displays the MFE output in a nice landscape like manner - the Utils script "relplot.pl" got a new commandline option "-a" that enables annotation of the accessibility in the structure plot - some changes in the build process now enable easier cross compilation of the Package - The example sourcecode in the reference manual got an update to comply with the specifications of ViennaRNA Package 2.x Programs: - G-Quadruplex prediction support in RNAfold, RNAcofold, RNALfold, RNAalifold, RNAeval and RNAplot this introduces a new commandline option '--gquad/-g' that enables G-quadruplex prediction. The dot-bracket notation for the structure output now contains an additional character '+' that indicates the presence of such a G-tetrad. Consecutive '+' signs always come in sets of 4 interspaced by some '.', marking the four G-runs and its linker sequences that comprise the quadruplex, respectively. - changes in RNAPKplex behavior and commandline options - new features and bugfixes in RNAplex and RNAsnoop - warning messages for all programs if an unsupported dangle option is selected Library: - LPfold got a new option to output its computations in split-mode - several G-Quadruplex related functions were introduced with this release - several functions for moves in an RNA landscape were introduced - a new function in alipfold.c now enables access to the partition function matrices of alipf_fold() - a different numeric approach was implement for concentration dependend co-folding to avoid instabilities which occured under certain circumstances | 25 January 2013, 13:50:52 UTC |
refs/tags/v2.0.7 | v2.0.7 | abdbf85 | - fix of bug in RNAplfold that caused segfault when specifying -O option - fix of misbehavior of RNAeval and RNAplot when called via tty | 18 May 2012, 09:21:00 UTC |
refs/tags/v2.0.6 | v2.0.6 | f3e2b22 | - bugfix bad type casting with gcc under MacOSX - bugfix for disappearing tri-/hexaloop contributions when read in from certain parameter files - bugfix for RNALfold that segfaulted on short strange sequences like AT+ repeats - change of RNA2Dfold output format for stoachstic backtracking | 20 April 2012, 13:19:40 UTC |
refs/tags/v2.0.5 | v2.0.5 | d3262c8 | - Restored RNALfoldz capability - Inserted latest changes from master branch (1.8.5) | 26 March 2012, 13:44:59 UTC |
refs/tags/v2.0.4 | v2.0.4 | 65e147f | - bugfix for RNAcofold and RNAalifold partition functions - restored Perl wrapper - bugfix for compiling without OpenMP support - restore backward compatibility in RNAlib when functions without the "_par()" suffix are called without setting global pf_scale to a reasonable value first | 08 March 2012, 15:56:02 UTC |
refs/tags/v2.0.3 | v2.0.3 | 48c40ba | Release of version 2.0.3 Changelog: Programs: - Added Boltzmann factor scaling in RNAsubopt, RNAalifold, RNAplfold and RNAcofold Library: - Restored threadsafety of folding matrix access in LPfold.c, alipfold.c, part_func.c, part_func_co.c and part_func_up.c - Added several new functions regarding threadsafe function calls in terms of concurrently changing the model details. The new functions with the suffix '_par' may now be used to pass an energy contribution datastructure filled with additional information about the model details. In this way, seperation from the global variables dangles, noLonelyPairs, noGU, no_closingGU, tetra_loop, temperature, logML is possible. Furthermore, the new functions also provide detachement from the global variables do_backtrack, fold_constrained This works for all implementations in fold.c part_func.c LPfold.c alipfold.c Basic support is provided in cofold.c part_func_co.c subopt.c However, since all cofolding functions currently rely on the global variable 'cut_point', they are not considered really threadsafe yet, i.e. a change in the cut_point while concurrent calculations take place will result in unpredictable results! Threadsafety of the remaining functions, regarding the above mentioned global variables will be incoorporated in upcoming versions See the reference manual of the RNAlib for more details (params.h, part_func.h, etc.) - Added pkg-config file in the distribution to allow easy checks for certain RNAlib2 versions, compiler flags and linker flags. This makes linking of third party programs against RNAlib2 much more easier. E.g. a call of 'pkg-config --modversion RNAlib2' reveals the version of the installed RNAlib. Developers who use autoconf may now take advantage of the different PKG_ macros to retrieve version, linker and compiler flags | 23 February 2012, 14:19:53 UTC |
refs/tags/v2.0.2 | v2.0.2 | bde7173 | Release of version 2.0.2 | 06 February 2012, 10:21:42 UTC |
refs/tags/v2.0.1 | v2.0.1 | c7cbca5 | Release of Version 2.0.1 | 15 January 2012, 11:40:20 UTC |
refs/tags/kinfold_new | kinfold_new | 965568e | release for developmentof new kinfoldby Daniel Oser | 13 October 2015, 12:27:02 UTC |