https://github.com/ViennaRNA/ViennaRNA
Branch name Release name Target Message Date
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
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