Changelog
v2.4.6
- Stabilize rounding of free energy output in RNAalifold
- API: Fix potential rounding errors for comparative free energies in eval.c and mfe.c
- API: Fix regression in exterior loop dangling end contributions for comparative base pair probabilities and Boltzmann sampling (introduced with v2.4.4)
- API: Fix regression with hard constrained base pairs for comparative structure prediction (introduced with v2.4.4)
- TESTS: Add basic tests for RNAalifold executable
- TESTS: Ignore ‘frequency of MFE structure’ in RNAcofold partition function checks
v2.4.5
- Allow for arbitrary number of input files in RNAfold
- Allow for parallel processing of input data in RNAfold (UNIX only, no Windows support yet)
- Add SHAPE reactivity support through commandline options for RNAplfold
- Fix unstructured domain motif detection in MFE, centroid, and MEA structures computed by RNAfold
- Limit allowed set of commands in command file for RNAcofold to hard and soft constraints
- API: Add functions to compute equilibrium probability of particular secondary structures
- API: Add dynamic string stream data type and associated functions
- API: Add priority-queue like data structure with unordered fill capability and ordered output callback execution
- API: Add functions to detect unstructured domain motifs in MFE, centroid, and MEA structures
- API: Fix bug in sliding-window partition function computation with SHAPE reactivity and Deigan et al. conversion method
- API: Fix application of ‘<’ and ‘>’ constraint symbols in dot-bracket provided constraints (was broken since v2.4.2)
- API: Fix MEA structure computation in the presence of unstructured domains
- API: Stabilize order of probability entries in EPS dot-plot files
- Fix compiler warnings on wrong type of printf() in naview.c
- Define VRNA_VERSION macro as string literal and add macros for major, minor, and patch numbers
- Stabilize parallel make of Mac OS X installer
- Add energy parameter set from Langdon et al. 2018
- Add autoconf checks for POSIX threads compiler/linker support
- SWIG: Fix ‘next’ is a perl keyword warnings for Perl5 wrapper
- SWIG: Catch errors and throw execptions whenever scripting language provided callback functions are not applicable or fail
- SWIG: Add keyword arguments and autodoc feature for Python/Python3 wrappers
v2.4.4
- Change verbose output for soft-constraints derived ligand binding motifs in RNAfold
- Allow for lowercase letters in ct2db input
- Fix bug in interior-like G-Quadruplex MFE computation for single sequences
- Fix autoconf switch to enable deprecation warnings
- Fix bug in eval_int_loop() that prevented propagation of energy evaluation for loops with nick in strands
- Fix several bugs for SHAPE reactivity related comparative partition function computations
- Fix annotation of PostScript output for soft-constraint derived ligand binding motifs in RNAfold
- Fix constraint indices for multibranch loops in unpaired probability computations of LPfold.c
- Fix dangling end contributions in comparative partition function for exterior loops
- API: Add simplified interface for vrna_pf_dimer()
- API: Move concentraton dependent implementation for co-folding to separate compile unit
- API: Add new API functions for exterior loop evaluations
- API: Add simplified interfaces for energy evaluation with G-Quadruplexes and circular RNAs
- API: Add findpath functions that allow for specification of an upper bound for the saddle point
- Add configure-time linker check for Python3 interface
- Add automatic CPP suggestions for deprecated function substitutes
- Major restucturing and constraints feature additions in loop type dependent energy evaluation functions
- Major restructuring in MFE implementations
- Major restructuring in PF implementations
- Minor fixes in Boltzmann sampling implementation
- SWIG: Fix wrappers for findpath() implementation
- SWIG: Add tons of energy evaluation wrappers
- SWIG: Fix configure-time check of Perl5 interface build capabilities
- SWIG: Wrap functions from walk.c and neighbor.c
- DOC: Add some missing references to manpages of executable programs
- REFMAN: Heavy re-ordering of the RNAlib reference manual
v2.4.3
- Fix handling of dangling end contribution at sequence boundaries for sliding window base pair probability computations
- Fix handling of base pair hard constraints in sliding-window implementations
- Fix sliding-window pair probability computations with multibranch-loop unpaired constraints
- Fix sliding-window non-specific base pair hard constraint implementation
- Fix probability computation for stochastic backtracking in RNAsubopt –stochBT_en output
- Fix regression in comparative structure prediction for circular RNAs
- Fix LDFLAGS for scripting language interfaces in corresponding Makefiles
- Stabilize partition function scaling by always using sfact scaling factor from model details
- Add –pf_scale commandling parameter to RNAplfold
- Add constraint framework for single sequence circular RNA structure prediction
- Add RNAfold test suite to check for working implementation of constraints for circular RNAs
- Add a brief contribution guideline CONTRIBUTING.md
- Prevent RNAplfold from creating inf/-inf output when solution set is empty with particular hard constraints
- Include RNAforester v2.0.1
v2.4.2
- Fix G-Quadruplex energy corrections in comparative structure energy evaluations
- Fix discrepancy in comparative exterior loop dangling end contribution of eval vs. MFE predictions
- Fix regression in RNAup unstructuredness and interaction energy computations
- Fix sequence length confusions when FASTA input contains carriage returns
- Fix build problems of RNAlocmin with older compilers
- Fix sliding-window hard constraints where single nucleotides are prohibited from pairing
- Fix dot-bracket output string length in sliding-window MFE with G-Quadruplexes
- Fix unpaired probability computations for separate individual loop types in LPfold.c
- Fix bad memory access in RNAsubopt with dot-bracket constraint
- Add full WUSS support for –SS_cons constraint option in RNAalifold
- Add commandline option to RNALalifold that enables splitting of energy contributions into separate parts
- Add missing hard constraint cases to sliding-window partition function implementation
- Add CSV output option to RNAcofold
- Use the same model details for SCI computations in RNAalifold
- Abort computations in vrna_eval_structure_v() if structure has unexpected length
- Use original MSA in all output generated by RNAalifold and RNALalifold
- API: Add new functions to convert dot-bracket like structure annotations
- API: Add various new utility functions for alignment handling and comparative structure predictions
- API: Add function vrna_strsplit() to split string into tokens
- API: Do not convert sequences of input MSA to uppercase letters in vrna_file_msa_read_record()
- API: Rename vrna_annotate_bp_covar() and vrna_annotate_pr_covar()
- API: Add new noLP neighbor generation
- SWIG: Add wrapper for functions in file_utils_msa.h
- SWIG: Add wrappers for vrna_pbacktrack() and vrna_pbacktrack5()
- SWIG: Add vrna_db_to_element_string() to scripting language interface
- REFMAN: Fix formula to image conversion in HTML output
v2.4.1
- Fix memory leak in fold_compound methods of SWIG interface
- Fix memory leaks in double ** returning functions of SWIG Perl5 interface
- Fix memory leak in vrna_ep_t to-string() function of SWIG interface
- Regression: Fix reverting pf_scale to defaults after vrna_exp_params_rescale()
- Regression: Fix homo-dimer partition function computation in RNAcofold
- Add unit tests for RNAcofold executable
- Add SHAPE reactivity support to RNAcofold
- Add SHAPE reactivity support to RNALalifold
v2.4.0
- Bump libsvm to version 3.22
- Print G-Quadruplex corrections in verbose mode of RNAeval
- Change behavior of RNAfold –outfile option to something more predictable
- Unify max_bp_span usage among sliding window prediction algorithms: RNAplfold, RNALfold, and RNALalifold now consider any base pair (i,j) with (j - i + 1) <= max_bp_span
- Add SHAPE reactivity data support to RNALfold
- Add commands-file support for RNALfold, RNAplfold (hard/soft constraints)
- Add RNAlocmin - Calculate local minima from structures via gradient walks
- Add RNA Bioinformatics tutorial (PDF version)
- Add hard constraints to sliding-window MFE implementations (RNALfold, RNALalifold)
- Add hard constraints to sliding-window PF implementations (RNAplfold)
- Add soft constraints to sliding-window MFE implementation for single sequences (RNALfold)
- Add soft constraints to sliding-window PF implementations (RNAplfold)
- Add SWIG interfaces for sliding-window MFE/PF implementations
- Add proper SWIG interface for alignment and structure plotting functions
- Add proper SWIG interface for duplexfold, duplex_subopt, and its comparative variants
- Add SWIG wrapper for vrna_exp_params_rescale()
- Add explicit destructor for SWIG generated vrna_md_t objects
- Add SWIG perl5 typemap for simple nested STL vectors
- Add dummy field in vrna_structured_domains_s
- Add note about SSE optimized code in reference manual
- Add SWIG interface for findpath implementation
- Add prepare() functions for ptypes-arrays and vrna_(exp_)param_t
- Add warnings for ignored commands in function vrna_commands_apply()
- Add callback featured functions for sliding window MFE and PF implementations
- Change default behavior of adding soft constraints to a vrna_fold_compound_t (store only)
- Several fixes with respect to G-Quadruplex prediction in sliding-window MFE recursions (single sequence and comparative implementation)
- Replace comparative sliding-window MFE recursions (All hits are reported to callback and can be filtered in a post-processing step)
- API: Remove E_mb_loop_stack() and introduce new function vrna_E_mb_loop_stack() as a replacement
- API: change data type of all constraint bit-flags from char to unsigned char
- API: change data type of a2s array in comparative structure prediction from unsigned short to unsigned int
- API: Change function parameter order in vrna_probs_window() to follow the style of other callback-aware functions in RNAlib
- Move sliding-window MFE implementations to new file mfe_window.c
- Fix building PDF Reference manual with non-standard executable paths
- Fix redefinition of macro ON_SAME_STRAND() in subopt.c
- Fix dangling end issues in sliding-window MFE implementations
- Fix regression for –canonicalBPonly switch in RNAfold/RNAcofold/RNAsubopt
- Fix building sliding-window MFE implementation without SVM support
- Fix parsing of STOCKHOLM 1.0 MSA files that contain MSA spanning multiple blocks
- Fix Alidot link in RNAalifold manpage
- Fix wrong pre-processor flags when enabling single-precision PF computations
- Fix unit testing perl5 interface by including builddir/tests in PERL5LIB path
- Fix buffer overflow in hairpin loop sequence motif extraction for circular RNAs
- Fix out-of-bounds memory access in neighbor.c
- Restore capability to compile stand-alone findpath utility
- Restore capability to use non-standard alphabets for structure prediction
- Restore old-API random number functions in SWIG interface
- Allow additional control characters in MAF MSA input that do not end a block
- Improve reference manual
- Make functions in
pair_mat.h
static inline
- Prevent users from adding out-of-range base pair soft constraints
- Inline print functions in color_output.inc
- Start documenting callback features in reference manual
- Re-write large portions of sliding-window PF implementation
- Introduce soft-constraint state flag
- Clean-up SWIG unit test framework
- Remove obsolete scripts ct2b.pl and colorrna.pl from src/Utils directory
- Remove old RNAfold tutorial
v2.3.5
- Fix duplication of output filename prefix in RNAfold
- Add V3.0 API for sliding window partition function (a.k.a. RNAPLfold)
- Add G-Quadruplex prediction to RNALalifold
- Add SWIG wrappers for callback-based sliding window comparative MFE prediction
- Add SSE4.1 multiloop decomposition for single sequence MFE prediction
- Enable RNAfold unit tests to run in paralllel
- Enable users to turn-off base pair probability computations in RNAcofold with -a option
- Split move set in neighbor.c
v2.3.4
- Fix G-Quadruplex probability computation for single sequences
- Fix double-free when using SHAPE reactivity data in RNAalifold
- Fix out-of-bounds access in strand_number array
- Fix weighting of SHAPE reactivity data in consensus structure prediction when fewer data than sequences are present
- Fix z-score output in RNALfold
- Substitute field name ‘A0’/’B0’ in data structure vrna_dimer_conc_s by ‘Ac_start’/’Bc_start’ to avoid clashes with termios.h (Mac OSX Python wrapper bug)
- Minimize usage of ‘unsafe’ sprintf() calls
- Enhance auto-id feature in executable programs
- Always sanitize output file names to avoid problems due to strange FASTA headers
- Lift restrictions of FASTA header length in RNAfold, RNAcofold, and RNAeval
- Add ViennaRNA/config.h with pre-processor definitions of configure time choices
- Add test-suite for RNAfold
- Add functions to procude colored EPS structure alignments
- Add function to write Stockholm 1.0 formatted alignments
- Add function to sanitize file names
- Add callback based implementation for sliding-window MFE prediction (single sequences, comparative structure prediction)
- Add fast API 3.0 implementations to generate structural neighbors and perform steepest descent / random walks (Thanks to Gregor!)
- Add parameter option to RNALalifold for colored EPS structure alignment and structure plot output
- Add parameter option to RNALalifold to write hits into Stockholm file
- Add parameter option to RNAalifold to write Stockholm 1.0 formatted output
- Add parameter option to RNAalifold to suppress stderr spam
- Add auto-id feature to RNAplot, RNALfold, RNAsubopt, RNAplfold, RNAheat
- Add SHAPE reactivity derived pseudo-energies as separate output in RNAalifold
- Add colored output to RNA2Dfold, RNALalifold, RNALfold, RNAduplex, RNAheat, RNAinverse, RNAplfold, and RNAsubopt
- Add command line parameters to RNAsubopt to allow for specification of input/output files
v2.3.3
- Fix multiloop contributions for comparative partition function
- Fix building python2 extension module for OSX
v2.3.2
- Fix pair probability plist creation with G-Quadruplexes
- Allow for specification of python2/3-config at configure time
- Fix init of vrna_md_t data structure after call to set_model_details()
- Fix bug in consensus partition function with hard constraints that force nucleotides to be paired
- Fix compilation of functions that use ellipsis/va_list
- Enable generic hard constraints by default
- Fix init of partition function DP matrices for unusually short RNAs
- Fix behavior of RNAplfold for unusually short RNAs
- Report SCI of 0 in RNAalifold when sum of single sequence MFEs is 0
- Avoid multiple includes of
pair_mat.h
- Add configure flag to build entirely static executables
v2.3.1
- Add description for how to use unstructured domains through command files to reference manual and RNAfold manpage
- Fix compilation issue for Windows platforms with MingW
- Add missing newline in non-TTY-color output of vrna_message_info()
- Fix regression in vrna_md_update() that resulted in incomplete init of reverse-basepair type array
- Extend coverage of generic hard constraints for partition function computations
- Fix scaling of secondary structure in EPS plot such that it always fits into bounding box
- Several fixes and improvements for SWIG generated scripting language interface(s)
v2.3.0
- Add grammar extension with structured and unstructured domains
- Add default implementation for unstructured domains to allow for ligand/protein binding to unpaired structure segments (MFE and PF for single sequences)
- Introduced command files that subsume constraint definition files (currently used in RNAfold and RNAcofold)
- Replace explicit calls to asprintf() with portable equivalent functions in the library
- Fix configure script to deal with situations where Perl module can’t be build
- Fix bug in doc/Makefile.am that prevented HTML installation due to long argument list
- Added utility functions that deal with conversion between different units
- Bugfix in SWIG wrapped generic soft constraint feature
- Add subopt() and subopt_zuker() methods to SWIG wrapped fold_compound objects
- Bugfix multiloop decomposition in MFE for circular RNAs
- Add separate function to compute pscore for alignments
- Renamed VRNA_VC_TYPE_* macros to VRNA_FC_TYPE_*
- Bugfix regression that prevented programs to fail on too long input sequences
- Extend EPS dot-plot in RNAfold to include motif/binding probabilities from unstructured domains
- Add variadic functions for error/warning/info message
- Add ID manipulation feature to RNAeval
- Extend API for soft constraint feature for more fine-grained control
- Add section on SWIG wrapped functions in reference manual
- Fix bug in interior loop computations when hard constraints result in non-canonical base pairs
v 2.2.10
- Do not ‘forget’ subopt results when output is not written to file handle and sorting is switched off
- Fix bad memory access in vrna_subopt() with sorted output
- Add SWIG wrappers for vrna_subopt_cb()
- Correctly show if C11 features are activated in configure status
- Fix autoconf checks to allow for cross compilation again
v 2.2.9
- Fix bug in partition function scaling for backward compatibility of ali_pf_fold()
- Stabilize v3.0 API when building RNAlib and third party program linking against it with compilers that use different C/C++ standards
- Add details on how to link against RNAlib to the reference manual
- Fix RNAlib2.pc
- Fix bug for temperature setting in RNAplfold
- Use -fflat-lto-objects for static RNAlib library to allow linking without LTO
- Fix interpretation of ‘P’ hard constraint for single nucleotides in constraint definition files
- Add ‘A’ command for hard constraints
- Fix several hard constraint corner-cases in MFE and partition function computation when nucleotides must not be unpaired
- Fix order of hard constraints when read from input file
- Allow for non-canonical base pairs in MFE and partition function computations if hard constraints demand it
- Fix behavior of –without-swig configure script option
- Fix bug in hard constraints usage of exterior loop MFE prediction with odd dangles
- Add parsers for Clustal, Stockholm, FASTA, and MAF formatted alignment files
- Enable RNAalifold to use Clustal, Stockholm, FASTA, or MAF alignments as input
- Lift restriction of sequence number in alignments for RNAalifold
- Enable ANSI colors for TTY output in RNAfold, RNAcofold, RNAalifold, RNAsubopt, and warnings/errors issued by RNAlib
- Add various new commandline options to manipulate sequence/alignment IDs in RNAfold, RNAcofold and RNAalifold
v 2.2.8
- 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
- Fix syntactic incompatibilities that potentially prevented compilation with compilers other than gcc
- dd 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
- 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
v 2.2.7
- Fix partition function scaling for long sequences in RNAfold, RNAalifold, and RNAup
- Fix backtracking issue in RNAcofold when –noLP option is activated
- Fix hard constraints issue for circular RNAs in generating suboptimal structures
- Rebuild reference manual only when actually required
v 2.2.6
- Plugged memory leak in RNAcofold
- Fixed partition function rescaling bug in RNAup
- Fixed bug in RNALfold with window sizes larger than sequence length
- Re-added SCI parameter for RNAalifold
- Fixed backtracking issue for large G-quadruplexes in RNAalifold
- Fixed missing FASTA id in RNAeval output
- Added option to RNAalifold that allows to specify prefix for output files
- Several fixes and additional functions/methods in scripting language interface(s)
- Added version information for scripting language interface(s)
- Some changes to allow for compilation with newer compilers, such as gcc 6.1
v 2.2.5
- 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 optional Python 3 interface
- 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 within SWIG target language
- Added optional subpackage Kinwalker
- Added several configure options to ease building and packaging under MacOS X
- Added new utility script RNAdesign.pl
v 2.2.4
- Fixed bug in RNAsubopt that occasionally produced cofolded structures twice
- Removed debugging output in preparations of consensus structure prediction datastructures
v 2.2.3
- Added postscipt annotations for found ligand motifs in RNAfold
- Added more documentation for the constraints features in RNAfold and RNAalifold
- Restore backward compatibility of get_alipf_arrays()
v 2.2.2
- Fix regression bug that occasionally prevented backtracking with RNAcofold –noLP
v 2.2.1
- 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
- Fix MEA computation when G-Quadruplex support is activated
- 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
v 2.2.0
- RNAforester is now of version 2.0
- New program RNApvmin to compute pseudo-energy pertubation vector that minimizes discrepancy between observed and predicted pairing probabilities
- SHAPE reactivity support for RNAfold, RNAsubopt, and RNAalifold
- Ligand binding to hairpin- and interior-loop motif support in RNAfold
- New commandline option to limit maximum base pair span for RNAfold, RNAsubopt, RNAcofold, and RNAalifold
- Bugfix in RNAheat to remove numerical instabilities
- Bugfix in RNAplex to allow for computation of interactions without length limitation
- Bugfix in RNAplot for simple layouts and hairpins of size 0
- (generic) hard- and soft-constraints for MFE, partition function, base pair probabilities, stochastic backtracking, and suboptimal secondary structures of single sequences, sequence alignments, and sequence dimers
- libsvm version as required for z-scoring in RNALfold is now 3.20
- Stochastic backtracking for single sequences is faster due to usage of Boustrophedon scheme
- First polymorphic functions vrna_mfe() , vrna_pf() , and vrna_pbacktrack() .
- The FLT_OR_DBL macro is now a typedef
- New functions to convert between different secondary structure representations, such as helix lists, and RNAshapes abstractions
- First object-oriented interface for new API functions in the scripting language interfaces
- new ViennaRNA-perl submodule that augments the Perl interface to RNAlib
- Ligand binding to hairpin- and interior-loop motif support in C-library and scripting language interfaces.
- Libraries are generated using libtool
- Linking of libraries and executables defaults to use Link Time Optimization (LTO)
- Large changes in directory structure of the source code files
v 2.1.9
- Fixed integer underflow bug in RNALfold
- Added Sequence Conservation index (SCI) option to RNAalifold
- Fixed bug in energy evaluation of dangling ends / terminal mismatches of exterior loops and multibranch loops
- 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
v 2.1.8
- Repaired incorporation of RNAinverse user provided alphabet
- Fix missing FASTA ID in RNAeval output
- prevent race condition in parallel calls of Lfold()
- Fixed memory bug in Lfold() that occured using long sequences and activated G-Quad support
- Added latest version of switch.pl
v 2.1.7
- Fixed bug in RNALfold -z
- Python and Perl interface are compiling again under MacOSX
- Fixed handling of C arrays in Python interface
- Added latest version of switch.pl
- Make relplot.pl work with RNAcofold output
v 2.1.6
- New commandline switches allow for elimination of non-canonical base pairs from constraint structures in RNAfold, RNAalifold and RNAsubopt
- 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
- New program ct2db allows for conversion of .ct files into dot-bracket notation (incl. pseudo-knot removal)
v 2.1.5
- Fix for discrepancy between special hairpin loop evaluation in partition functions and MFE
v 2.1.4
- Fix of G-quadruplex support in subopt()
- Fix for discrepancy between special hairpin loop evaluation in partition functions and MFE
v 2.1.3
- RNAfold: Bugfix for ignoring user specified energy parameter files
- RNAcofold: Bugfix for crashing upon constrained folding without specifying a constraint structure
- RNAsubopt: Added G-quadruplex support
- RNAalifold: Added parameter option to specify base pair probability threshold in dotplot
- Fix of several G-quadruplex related bugs
- Added G-quadruplex support in subopt()
v 2.1.2
- RNAfold: Bugfix for randomly missing probabilities in dot-plot during batch job execution
- RNAeval: Bugfix for misinterpreted G-quadruplex containing sequences where the quadruplex starts at nucleotide 1
- RNAsubopt: Slight changes to the output of stochastic backtracking and zuker subopt
- Fix of some memory leaks
- Bugfixes in zukersubopt() , assign_plist_from_pr()
- New threadsafe variants of putoutpU_prob*() for LPfold()
- Provision of python2 interface support.
v 2.1.1
- Bugfix to restore backward compatibility with ViennaRNA Package 1.8.x API (this bug also affected proper usage of the the perl interface)
v 2.1.0
- G-Quadruplex support in RNAfold, RNAcofold, RNALfold, RNAalifold, RNAeval and RNAplot
- 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
- new function in alipfold.c now enables access to the partition function matrices of alipf_fold()
- different numeric approach was implement for concentration dependend co-folding to avoid instabilities which occured under certain circumstances
v 2.0.7
- Bugfix for RNAplfold where segfault happened upon usage of -O option
- Corrected misbehavior of RNAeval and RNAplot in tty mode
v 2.0.6
- Bugfix for bad type casting with gcc under MacOSX (resulted in accidental “sequence too long” errors)
- 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 stochastic backtracking
v 2.0.5
- Restored z-score computation capabilities in RNALfold
v 2.0.4
- Bugfix for RNAcofold partition function
- Perl wrapper compatibility to changed RNAlib has been restored
- Backward compatibility for partition function calls has been restored
v 2.0.3
- Bugfix for RNAalifold partition function and base pair probabilities in v2.0.3b
- Added Boltzmann factor scaling in RNAsubopt, RNAalifold, RNAplfold and RNAcofold
- Bugfix for alipfold() in v2.0.3b
- 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
- Added pkg-config file in the distribution to allow easy checks for certain RNAlib2 versions, compiler flags and linker flags.
v 2.0.2
- added support for Boltzmann factor scaling in RNAfold
- fixed fastaheader to filename bug
- plugged some memory leaks
v 2.0.1
- First official release of version 2.0
- included latest bugfixes
__History__
2011-03-10 Ronny Lorenz ronny@tbi.univie.ac.at
- new naming scheme for all shipped energy parameter files
- fixed bugs that appear while compiling with gcc under MacOS X
- fixed bug in RNAup –interaction-first where the longer of the first two sequences was taken as target
- added full FASTA input support to RNAfold, RNAcofold, RNAheat, RNAplfold RNALfoldz, RNAsubopt and RNALfold
2010-11-24 Ronny Lorenz ronny@tbi.univie.ac.at
- first full pre-release of version 2.0
2009-11-03 Ivo Hofacker ivo@tbi.univie.ac.at
2009-09-09 Ivo Hofacker ivo@tbi.univie.ac.at
- Fix bug in RNAplfold when -u and -L parameters are equal
- Fix double call to free_arrays() in RNAfold.c
- Improve drawing of cofolded structures
2009-05-14 Ivo Hofacker ivo@tbi.univie.ac.at
- Fix occasional segfault in RNAalifold’s print_aliout()
2009-02-24 Ivo Hofacker ivo@tbi.univie.ac.at
- Add -MEA options to RNAfold and RNAalifold
- change energy_of_alistruct to return float not void
2009-02-24 Ivo Hofacker ivo@tbi.univie.ac.at
- RNAfold will draw structures unless -noPS is used (no more “structure too long” messages)
- Restore the “alifold.out” output from RNAalifold -p
- RNAalifold -circ did not work due to wrong return type
- Accessibility calculation with RNAplfold would give wrong results for u<=30
2008-12-03 Ivo Hofacker ivo@tbi.univie.ac.at
- Add zuker style suboptimals to RNAsubopt (-z)
- get_line() should be much faster when reading huge sequences (e.g. whole chromosomes for RNALfold)
2008-08-12 Ivo Hofacker ivo@tbi.univie.ac.at
- Add Ribosum matrices for covariance scoring in RNAalifold
2008-06-27 Ivo Hofacker ivo@tbi.univie.ac.at
- Change RNAalifold to used berni’s new energy evaluation w/o gaps
- Add stochastic backtracking in RNAalifold
2008-07-04 Ivo Hofacker ivo@tbi.univie.ac.at
- modify output of RNAup (again). Program reading RNAup output will have to updated!
2008-07-02 Ivo Hofacker ivo@tbi.univie.ac.at
- RNAplfold now computes accessibilities for all regions up to a max length simultaneously. Slightly slower when only 1 value is needed, but much faster if all of them are wanted. This entails a new output format. Programs reading accessibility output from RNAplfold need to be updated!
2008-03-31 Stephan Bernhart berni@tbi.univie.ac.at
- add cofolding to RNAsubopt
2008-01-08 Ivo Hofacker ivo@tbi.univie.ac.at
- ensure circfold works even for open chain
2007-12-13 Ulli Mueckstein ulli@tbi.univie.ac.at
- upate RNAup related files RNAup can now include the intramolecular structure of both molecules and handles constraints.
2007-12-05 Ronny Lorenz ronny@tbi.univie.ac.at
- add circfold variants in part_func.c alipfold.c subopt.c
2007-09-19 Ivo Hofacker ivo@tbi.univie.ac.at
- compute the controid structure of the ensemble in RNAfold -p
- fix a missing factor 2 in mean_bp_dist() . CAUTION ensemble diversities returned by RNAfold -p are now twice as large as in earlier versions.
2007-09-04 Ivo Hofacker ivo@blini.tbi.univie.ac.at
- fix a bug in Lfold() where base number n-max-4 would never pair
2007-08-26 Ivo Hofacker ivo@tbi.univie.ac.at
- add RNAaliduplex the alignment version of RNAduplex
- introduce a minimal distance between hits produced by duplex_subopt()
2007-07-03 Ivo Hofacker ivo@tbi.univie.ac.at
2007-06-23 Ivo Hofacker ivo@tbi.univie.ac.at
2007-04-30 Ivo Hofacker ivo@tbi.univie.ac.at
- add RNAup to distribution
2007-04-15 Ivo Hofacker ivo@tbi.univie.ac.at
- fix segfault in colorps output (thanks to Andres Varon)
2007-03-03 Ivo Hofacker ivo@tbi.univie.ac.at
- avoid unnormalized doubles in scale[], big speedup for pf_fold() on very long sequences
2007-02-03 Ivo Hofacker ivo@tbi.univie.ac.at
- RNAalifold can now produce colored structure plots and alignment plots
2007-02-01 Ivo Hofacker ivo@tbi.univie.ac.at
- Fix segfault in RNAplfold because of missing prototype
2006-12-01 Ivo Hofacker ivo@tbi.univie.ac.at
- RNAduplex would segfault when no structure base pairs are possible
2006-08-22 Ivo Hofacker ivo@tbi.univie.ac.at
- add computation stacking probabilities using RNAfold -p2
- add -noPS option for NRAfold to supress drawing structures
2006-08-09 Stephan Bernhart berni@tbi.univie.ac.at
- RNAplfold can now compute probabilites of unpaired regions (scanning version of RNAup)
2006-06-14 Ivo Hofacker ivo@tbi.univie.ac.at
- compile library with -fpic (if available) for use as shared library in the Perl module.
- fix another bug when calling Lfold() repeatedly
- fix switch cmdline parsing in RNAalifold (-mis implied -4)
- fix bug in cofold() with dangles=0
2006-05-08 Ivo Hofacker ivo@tbi.univie.ac.at
- fix segfault in Lfold() when calling repeatedly
- fix structure parsing in RNAstruct.c (thanks to Michael Pheasant for reporting both bugs)
- add duplexfold() and alifold() to Perl module
- distinguish window size and max pair span in LPfold
2006-04-05 Ivo Hofacker ivo@tbi.univie.ac.at
- fix performance bug in co_pf_fold()
- use relative error for termination of Newton iteration
2006-03-02 Ivo Hofacker ivo@tbi.univie.ac.at
2006-01-18 Ivo Hofacker ivo@tbi.univie.ac.at
- cleanup berni partition cofold code, including several bug fixes
2006-01-16 Ivo Hofacker ivo@tbi.univie.ac.at
2005-11-07 Ivo Hofacker ivo@tbi.univie.ac.at
- add new utilities colorna and coloraln
2005-10-11 Christoph Flamm xtof@tbi.univie.ac.at
2005-07-24 Ivo Hofacker ivo@tbi.univie.ac.at
- fix a few memory problems in structure comparison routines
2005-04-30 Ivo Hofacker ivo@blini.tbi.univie.ac.at
- add folding of circular RNAs
2005-03-11 Ivo Hofacker ivo@blini.tbi.univie.ac.at
- add -mis option to RNAalifold to give “most informative
- sequence” as consensus
2005-02-10 Ivo Hofacker ivo@tbi.univie.ac.at
2004-12-22 Stephan Bernhart berni@tbi.univie.ac.at
- add partition function version of RNAcofold
2004-12-23 Ivo Hofacker ivo@tbi.univie.ac.at
- add RNApaln for fast structural alignments (RNApdist improvement)
2004-08-12 Ivo Hofacker ivo@tbi.univie.ac.at
- fix constrained folding in stochastic backtracking
2004-07-21 Ivo Hofacker ivo@tbi.univie.ac.at
- add RNAduplex, to compute hybrid structures without intra-molecular pairs
2004-02-09 Ivo Hofacker ivo@tbi.univie.ac.at
- fix bug in fold that caused segfaults when using Intel compiler
- add computation of ensemble diversity to RNAfold
2003-09-10 Ivo Hofacker ivo@tbi.univie.ac.at
- add annotation options to RNAplot
2003-08-04 Ivo Hofacker ivo@tbi.univie.ac.at
- stochastic backtracking finally works. Try e.g. RNAsubopt -p 10
2003-07-18 Ivo Hofacker ivo@tbi.univie.ac.at
- add relplot.pl and rotate_ss.pl utilities for reliability annotation and rotation of rna structure plots
2003-01-29 Ivo Hofacker ivo@tbi.univie.ac.at
- add RNALfold program to compute locally optimal structures with maximum pair span.
- add RNAcofold for computing hybrid structure
2002-11-07 Ivo Hofacker ivo@tbi.univie.ac.at
2002-10-28 Ivo Hofacker ivo@tbi.univie.ac.at
- Improved Perl module with pod documentation; allow to write things like ($structure, $energy) = RNA::fold($seq); Compatibility warning: the ptrvalue() and related functions are gone, see the pod documentation for alternatives.
2002-10-29 Ivo Hofacker ivo@tbi.univie.ac.at
- added svg structure plots in PS_dot.c and RNAplot
2002-08-15 Ivo Hofacker ivo@tbi.univie.ac.at
- Improve reading of clustal files (alifold)
- add a sample alifold.cgi script
2001-09-18 Ivo Hofacker ivo@tbi.univie.ac.at
- moved suboptimal folding into the library, thus it’s now accessible from the Perl module
2001-08-31 Ivo Hofacker ivo@tbi.univie.ac.at
2001-04-30 Ivo Hofacker ivo@tbi.univie.ac.at
- switch from handcrafted makefiles to automake and autoconf
2001-04-05 Ivo Hofacker ivo@tbi.univie.ac.at
- added PS_rna_plot_a to produce structure plots with annotation
2001-03-03 Ivo Hofacker ivo@tbi.univie.ac.at
- add alifold; predict consensus structures from alignment
2000-09-28 Ivo Hofacker ivo@tbi.univie.ac.at
- add -d3 option to RNAfold for co-axial stacking