Below, you'll find a list of notable changes for each version of the ViennaRNA Package.

• Fix structure output in RNAeval for more than 2 interacting RNAs
• Fix wrong application of soft constraints to single sequences in RNAcofold
• Add --benchmark option for RNAfold
• Add --benchmark option for RNAalifold

• API: Fix wrong application of soft constraints to single sequences in vrna_mfe_dimer()
• API: Restore backward compatibility issues after early removal of vrna_constraints_add_SHAPE() and others
• API: Re-use energy parameters for successive vrna_params() / vrna_exp_params() calls if possible
• API: Add negative log probability method (information content) as generic probing data strategy
• API: Add vrna_math_dbl_chain() to allow for chaining vrna_math_dbl* functions
• API: Add function to allow for chaining probing data strategies
• API: Change structure benchmark numbers to double type

• Fix misplaced 'i' in rna_turner2004.par

• Allow for FASTA header changes in ct2db
• Fix constraints parsing in RNAsubopt
• Add new command line options for structure probing data to RNAfold and RNAsubopt

• API: Refactor structure probing data API to support multiple data at once, position-wise weighting, user-defined reactivity-to-energy strategies and more
• API: Refactor hard constraint wrappers
• API: Add ViennaRNA/math/ to provide several useful mathematical functions
• API: Add vrna_str_to_dbl_array()
• API: Add vrna_file_doubles_read()
• API: Fix backtracking issues in exterior loop
• API: Fix backtracking issues with odd dangles
• API: Fix segmentation fault in vrna_pt_pk_remove()
• API: Fix vrna_plist() and vrna_ptable() to deal with malformed input
• API: Fix soft constraints access in backtracking of QM2 (Boltzmann sampling)
• SWIG: Add wrappers for concentration dependency computations
• SWIG: Fix RNA.fold_compound.bpp() output for multistrand base pair probabilities
• SWIG: Do not return symmetric pair probability matrix by default
• SWIG: Fix Python object ownership in callbacks for unstructured domains, direct soft constraints and landscape moves

• Update dlib to version 20.0
• Overall improvements to the documentation
• Fix energy parameter file markup
• Fix compilation with compilers that default to C23
• Update swig requirement to 4.2.0
• Fix compilation without libsvm
• Update breathe to version v5.0.0a5
• Add probing data priors (paired and unpaired) for 1M7 and DMS

• Add hard limit for number of input structures in RNAdistance
• Add counter example settings to RNAalifold
• Add covariance annotation legend to RNAplot layout plots for MSA input
• Add covariance annotation legend to RNALalifold layout plots
• Adapt structure conservation coloring and add legend in alignment output of RNAplot, RNAalifold, and RNALalifold
• Add RNAconsensus Python program that will eventually replace refold.pl
• Add --log-file, --log-level, --log-call and --log-time command line options to executable programs
• Add --betaScale and --pfScale options to and rescale Boltzmann factors in RNAPKplex
• Add support for G-Quadruplexes in circular RNAs for RNAfold, RNAalifold, and RNAeval
• Change RNAplot command line argument -o to -f
• Add --random-seed option to RNAsubopt and RNAalifold to specify seed for random number generator

• API: Add circular RNA G-Quadruplex support
• API: Add structure prediction benchmark functions vrna_compare_structure() and vrna_compare_structure_pt()
• API: Add vrna_annotate_covar_pt() that allows for specifying number of counter examples
• API: Add structure conservation legend to EPS consensus structure layout plots
• API: Add vrna_string_make_space_for() and vrna_string_available_space() functions in ViennaRNA/datastructures/string.h
• API: Add vrna_file_PS_aln_opt() to allow for changing conservation coloring
• API: Add flexible log message system to avoid spam on stderr and stdout
• API: Add (generic) compressed sparse row (CSR) matrix implementation
• API: Add Eddy 2014 approach to incorporate experimental probing data (using Gaussian KDE)
• API: Add generic support for experimental probing data via new API in ViennaRNA/probing/basic.h
• API: Add full probing data support for consensus structure prediction
• API: Add vrna_sc_multi_cb_add_comparative() to allow for multi callback soft constraints in comparative structure predictions
• API: Add vrna_fold_compound_t to parameters passed to recursion status callback
• API: Add M2 matrices in favor of M1 for global MFE and partition function computations
• API: Add safeguard to vrna_array_free()
• API: Add vrna_pairing_tendency() as replacement for vrna_db_from_probs()
• API: Group related API symbols and header files into specific subdirectories
• API: Allow base pair hard constraints via commands file where j = i + 1
• API: Refactor vrna_pk_plex() accessibility computations
• API: Refactor backtracking implementations and API, now located under ViennaRNA/backtrack/
• API: Refactor experimental probing data (SHAPE) implementations, now located under ViennaRNA/probing/
• API: Refactor auxiliary grammar extension API, now located under ViennaRNA/grammar/
• API: Refactor G-Quadruplex implementation and fix existing bugs and numerical issues in corresponding energy evaluation
• API: Refactor verbose vrna_eval*() implementations
• API: Refactor structure plotting API and add unified structure plotting function vrna_plot_structure()
• API: Remove exit() calls from RNAlib
• API: Change behavior and parameter order for vrna_hc_add_bp_strand()
• API: Change behavior and parameters of vrna_hc_add_up_strand()
• API: Unify backtracking matrix flags
• API: Use vrna_array() based base pair and backtrack stacks for MFE implementations
• API: Introduce entropic penalty for unpaired circular RNAs (may be switched off by model settings circ_penalty flag)
• API: Deprecate vrna_message_info(), vrna_message_warning(), and vrna_message_error() in favor of new loggin system
• API: Fix vrna_neighbor_diff*() insertion moves
• API: Fix MFE inside recursion for multiloop unpaired positions
• API: Fix vrna_hx_from_ptable() when provided hairpins of length 0
• API: Fix vrna_hx_merge() to support pseudoknotted helices
• API: Fix re-use of previous energy parameters upon model changes in duplex.c
• API: Fix re-use of previous energy parameters upon model changes in c_plex.c
• API: Fix re-use of previous energy parameters upon model changes in plex.c
• API: Fix re-use of previous energy parameters upon model changes in ali_plex.c
• API: Fix re-use of previous energy parameters upon model changes in snofold.c
• API: Fix re-use of previous energy parameters upon model changes in snoop.c
• API: Fix mismatch and dangling end energies in sc_cb_mod.c for modified base support
• API: Fix Zuker-style subopt backtracking
• API: Fix bug in vrna_strdup_vprintf() that resulted in losing parmeters upon consecutive calls
• API: Fix default exterior loop MFE soft constraints for comparative structure prediction
• SWIG: Use av_len() instad of av_top_index() for Perl 5 to support perl5 < v5.18.0
• SWIG: Fix compilation issues for Python 3.12 due to use of SWIG_Python_str_AsChar()
• SWIG: Add wrapper for vrna_hx_merge()
• SWIG: Add wrapper for vrna_sc_multi_cb_add()
• SWIG: Add wrappers for vrna_hc_add_bp_strand() and vrna_hc_add_up_strand()
• SWIG: Add file I/O constants
• SWIG: Add wrappers for structure prediction benchmark functions
• SWIG: Add wrappers for log message system
• SWIG: Add wrapper for vrna_stack_prob()
• SWIG: Add wrappers for new probing data API
• SWIG: Add wrapper for vrna_n_multichoose_k()
• SWIG: Return int instead of float for eval_structure_pt_simple()

• AUTOCONF: Fix several autoconf/automake related issues
• AUTOCONF: Add ./configure --enable-debug option that prevents removal of vrna_log_debug() message from RNAlib
• Add m5C JSON energy parameter file
• Add N1-methylpseudouridine JSON energy parameter file
• Add OpenMP library flags to RNAlib2.pc
• DOC: Improve document structure
• Bump libsvm to version 3.35
• Remove RNA-Tutorial since it is now included as part of the reference manual
• Remove Python 2 builds from MacOSX installer

• Fix C++17 compilation issue with kinwalker
• Fix potential compilation issues with C++20 in RNAforester frontend
• Refactor and correct spelling issues in man pages for several executable programs

• API: Add shift move support to vrna_move_neighbor_diff*() functions
• API: Fix char array initialization in snoop.c
• API: Fix potentially leaking file pointer in vrna_file_msa_read()
• API: Fix potentially leaking memory in rnaplot_EPS()
• API: Fix potential use of uninitialized variable in vrna_rotational_symmetry_db_pos()
• API: Fix soft constraints issue in external loop of vrna_subopt*()
• SWIG: Add swig class output parameter typemap for Python
• SWIG: Add __hash__() and __eq__() methods for wrapped _vrna_move_t in Python
• SWIG: Return var_array<vrna_move_t> objects in Python wrapped vrna_neighbors() and vrna_move_neighbor_diff()
• SWIG: Refactor file handle wrapping between Python 3 and C
• SWIG: Fix var_array Python slices and associated memory leak
• SWIG: Fix bogus delete/free() calls in swig interface
• Add requirements to build RNAlib with MSVC for Windows
• Remove unused code in RNApuzzler

• DOC: Transition reference manual from doxygen to sphinx via breathe bridge
• DOC: Merge documentation of C-API and Python API
• DOC: Merge parts of tutorial into reference manual
• AUTOCONF: Refactor autoconf checks for capability to build reference manual
• AUTOCONF: Deactivate build of RNAxplorer if lapack requirements are not met

• Make JSON parser integral part of ViennaRNA library
• API: Move modified energy parameters into 'modified_base' object in JSON file(s)
• SWIG: Enable stand-alone build of Python interface (for PyPI)

• Add enthalpy and terminal end values for predicted stacks with dihydrouridine
• TESTS: Allow for using pytest to test the Python 3 interface

• Fix preparation of input sequences for modified base support in RNAcofold

• Fix energy corrections for modified base support when unmodified base is not the same as fallback base, e.g. in the case of inosine
• Add soft constraints to multifold external loop decomposition
• Add soft constraints preparation stage callback
• SWIG: Fix fc.sc_add_bp() propagation of constraint values
• SWIG: Wrap energy parameter file strings

• TESTS: Add modified base tests on duplex data with I-C and A-Psi pairs from publications

• Fix double free corruption in RNAdos
• Fix compilation issues due to use of uint instead of unsigned int for RNAxplorer
• Fix compilation issues for RNAxplorer when OpenMP is unavailable

• AUTOCONF: Update autoconf macros
• Update Debian-based packaging rules

• Add modified base input support to RNAfold
• Add modified base input support to RNAplfold
• Add modified base input support to RNALfold
• Add modified base input support to RNAcofold
• Add modified base input support to RNAsubopt
• Fix missing strand separators in RNAsubopt when applied to multiple interacting sequences
• Fix sorted output in RNAsubopt with --gquad option
• Allow for only -Fp in RNAinverse instead of always activating -Fm
• Fix default value of RNAinverse -R option in manpage
• Restructure --*help output and man pages for most executable programs
• Allow for cation concentration (Na+) changes in most executable programs (default 1.021M)
• Allow for at least as many threads as CPUs are configured if maximum thread number detection fails
• Fix alignment input parsing in refold.pl
• Add RNAxplorer program to the distribution

• API: Extend model_details to allow for salt concentration changes
• API: Add functions for salt concentration change derived energy corrections in ViennaRNA/params/salt.h
• API: Add arbitrary modified base support (vrna_sc_mod()) via soft constraints mechanism and JSON input data
• API: Add Pseuoduridine-A parameters via soft constraints callback
• API: Add Dihydrouridine parameters via soft constraints callback
• API: Add inosine-U and inosine-C parameters via soft constraints callback
• API: Add m6A parameters via soft constraints callback mechanism
• API: Add 7DA modification support via soft constraints
• API: Add Purine (nebularine) modification support
• API: Add new soft constraints multi-callback dispatcher
• API: Add dynamic array data structure utilities
• API: Add string data structure utilities
• API: Add vrna_strchr() function
• API: Fix potential problems in free_dp_matrices() of LPfold.c
• API: Fix z-score initialization in vrna_Lfoldz() amd vrna_mfe_window_zscore_cb()
• API: Fix file close issue in vrna_file_commands_read()
• API: Fix backtracking issue in Zuker subopt
• API: Fix missing soft constraints callback execution in Zuker subopt
• API: Fix enumeration of G-quadruplexes in vrna_subopt() and vrna_subopt_cb()
• API: Fix constraints bug for exterior loop in boltzmann sampling
• API: Allow for enforcing 'must pair' constraint (|) in dot-bracket constraints strings
• API: Fix discrepancy between global and local folding in how hard constraints for unpaired bases and non-specific pairing are applied
• API: Refactor function typdefs to make them actual function pointer typedefs
• SWIG: Fix Python 3 wrapper suffix issue
• SWIG: Fix Perl 5 wrapper for vrna_ud_prob_get()
• SWIG: Only accept upper triangular part of matrix input in fc.sc_bp_add()
• SWIG: Use var_array instead of tuples for Python RNA.ptable()
• SWIG: Add Python wrapper for vrna_move_neighbor_diff()
• SWIG: Add Python docstrings generated from doxygen documentation of C-library

• Update libsvm to version 3.31
• Update dlib to version 19.24
• Adapt Debian dependencies
• Fix compilation issues with RNAforester
• AUTOCONF: Fix requirement checks when SVM support is deactivated and swig is missing
• AUTOMAKE: Add auto parameters for -flto compile/link flags
• AUTOCONF: Require C++17 due to dependencies to compile DLIB
• AUTOCONF: Deactivate Python 2 bindings by default

• Refactor ct2db program to allow for pseudoknots in output structure

• API: Fix MEA computation for G-quadruplex predictions
• API: Fix memory leak in hard constraints container
• API: Fix RNApuzzler edge-case that resulted in segmentation faults
• API: Fix invalid memory access in vrna_strjoin()
• API: Revisit generic soft constraints for sliding-window base pair probability computations
• API: Enable to overwrite automatic unpaired probability determination in MEA computation
• API: Add #VRNA_PLIST_TYPE_UNPAIRED and #VRNA_PLIST_TYPE_TRIPLE identifiers for vrna_ep_t
• API: Add vrna_init_rand_seed() to initialize RNG with seed
• API: Add vrna_zsc_compute_raw() to obtain mean and sd for Z-score computation
• API: Add vrna_file_connect_read_record() function to parse connectivity table (*.ct) files
• API: Add vrna_strtrim() function
• API: Update sanity checks for input in vrna_pbacktrack_sub*()
• API: Allow for pseudo-knots in vrna_db_from_ptable()
• API: Do not use min_loop_size = 0 for multi strand interaction prediction
• API: Remove unnecessary uses of min_loop_size at multiple locations
• API: Deprecate cutpoint member of vrna_fold_compound_t and prepare for 5'/3' encoding
• API: Refactor sequence addition/preparation for vrna_fold_compound_t
• DOC: Update documentation
• SWIG: Add simple dot-plot file wrapper plot_dp_EPS()
• SWIG: Add sequence, sequence_encoding and sequence_encoding2 attributes to fold_compound objects
• SWIG: Fix RNG wrapping and initialize RNG upon module load and update associated functions
• SWIG: Add more access to member variable arrays for various objects used throughout the library
• SWIG: Add memory efficient wrapper for dynamically allocated arrays and matrices
• SWIG: Shadow pair table data structure for efficient interactions between C and target languages
• SWIG: Expose hard constraints members in fold_compound objects
• SWIG: Add exp_E_ext_stem() method (vrna_exp_E_ext_stem()) to fold_compound objects
• SWIG: Expose DP matrices within fold_compound objects
• SWIG: Fix memory leak in wrapper for vrna_db_from_ptable()

• Update dlib to version 19.23
• DOC: Update doxygen.conf for version 1.9.2
• AUTOCONF: Factor-out Naview layout algorithm to allow for deactivating the Naview layout algorithm at configure-time
• AUTOCONF: Make LaTeX checks more portable and update LaTeX package checks
• AUTOCONF: Check whether we can build the swig interface when SVM support is deactivated
• AUTOCONF: Fix condition check for CLA build

• Add RNAmultifold program to compute secondary structures for multiple interacting RNAs
• Add multistrand capabilities to RNAeval
• Add multistrand capabilities to RNAsubopt
• Replace RNAcofold with a wrapper to RNAmultifold
• Fix computation of BB homodimer base pair probabilities in RNAcofold

• API: Fix use of undefined values in deprecated function PS_dot_plot()
• API: Fix probability computations for unstructured domains within multibranch loops
• API: Fix index error in ensemble defect computations
• API: Fix hard constraints behavior on non-specific base pairing
• API: Fix segmentation fault for short input sequences in vrna_hx_from_ptable()
• API: Fix memory leak in static rna_layout() function
• API: Fix corner-case in covariance score computation on sequence alignments that determines which alignment columns may pair and which don't
• API: Add MFE computations for multiple interacting strands
• API: Add partition function computations for multiple interacting strands
• API: Add base pair probability computations for multiple interacting strands
• API: Add suboptimal structure prediction for multiple interacting strands
• API: Add multistrand capabilities to vrna_eval*() functions
• API: Add new function vrna_equilibrium_conc() fir concentration dependency computations of multiple interacting strands with dlib backend
• API: Add vrna_equilibrium_constants() function to obtain equilibrium constants for different complexes of multiple interacting strands
• API: Add function vrna_pf_add() to add ensemble free energies of two ensembles
• API: Add function vrna_pf_substrands() to get ensemble free energies for complexes up to a specific number of interacting strands
• API: Add function vrna_n_multichoose_k() to obtain a list of k-combinations with repetition
• API: Add vrna_cstr_discard() function to allow for discarding char streams prior to flushing
• API: Add vrna_bp_distance_pt() function to allow for base pair distance computation with pseudo-knots
• API: Add functions vrna_pbacktrack_sub*() to allow for stochastic backtracing within arbitrary sequence intervals
• API: Add functions vrna_boustrophedon() and vrna_boustrophedon_pos() to generate lists of or obtain values from sequences of Boustrophedon distributed integer numbers
• API: Add vrna_pscore() and vrna_pscore_freq() functions to obtain covariance score for particular alignment columns
• API: Rewrite Zuker suboptimals implementation
• API: Remove old cofold implementations
• API: Make type attribute of vrna_mx_mfe_t and vrna_mx_pf_t a constant
• API: Guard more functions in utils/structure_utils.c against NULL input
• API: Rename vrna_E_ext_loop() to vrna_eval_ext_stem()
• API: Use v3 typedefs in dot-plot function declarations
• SWIG: Fix Python 3 file handle as optional argument in eval* functions and methods
• SWIG: Add wrapper for vrna_pf_add()
• SWIG: Add wrapper for vrna_hx_from_ptable()
• SWIG: Add wrapper for vrna_db_from_probs()

• Update libsvm to version 3.25
• Make Python 3.x the default Python for the scripting languange interfaces
• Add Python3 capability for Mac OS X installer builds
• TESTS: Create TAP driver output for all unit tests (library, executables, SWIG interfaces)
• Remove compile-time switch to deactivate Boustrophedon backtracing scheme (this is the status-quo now)
• Add Contributors License Agreement (CLA) to the Package in doc/CLA/

• Fix and refactor RNApkplex program
• Fix occasional backtracing errors in RNALalifold
• Restrict available dangling end models in RNALalifold to 0 and 2
• Prevent segmentation faults upon bogus input data in RNAfold, RNAalifold, RNAcofold, RNAheat, and RNAeval
• Free MFE DP matrices in RNAsubopt Boltzmann sampling when not required anymore

• API: Add vrna_abstract_shapes() and vrna_abstract_shapes_pt() functions to convert secondary structures into their respective abstract shape notation ala Giegerich et al. 2004
• API: Add functions vrna_seq_reverse() and vrna_DNA_complement() to create reverse complements of a sequence
• API: Add more soft constraint handling to comparative structure prediction
• API: Add generic soft constraints for sliding window comparative MFE backtracing
• API: Add vrna_ensemble_defect_pt() that accepts pair table input instead of dot-bracket string to allow for non-nested reference structures
• API: Add failure/success return values to generic soft constraints application functions
• API: Refactor RNAPKplex implementation by better using constraints framework and moving out many parts from RNAPKplex.c into RNAlib as separate re-usable functions
• API: Fix energy contributions used in RNAPKplex implementations
• API: Fix energy evaluation for cofolding with dangle model 1
• API: Fix wrong arithmetic usage for PF variant of combined generic and simple soft constraints applied to external loops
• API: Fix memory size in #vrna_fold_compound_t initialization
• API: Fix bogus memory access for comparative prediction when preparing hard constraints
• API: Fix wrong index usage in hard constraints for comparative base pair probability computations of internal loops
• API: Fix G-Quadruplex contributions as part of multibranch loops in single sequence base pair probability computations
• API: Fix multibranch loop MFE decomposition step for multiple strand cases
• API: Fix external loop generic hard constraint index updating for partition function computations
• API: Fix memory allocation for auxiliary grammar data structure
• API: Fix incorporation of auxiliary grammar contrib for closing pairs in sliding-window MFE computation
• API: Fix DP matrix intitialization in sliding window MFE computations (fixes occasional backtracing issues in comparative sliding-window MFE computations)
• API: Make vrna_sc_t.type attribute a constant
• API: Remove upper-triangular hard constraint matrix in favor of full matrix
• API: Always ensure sane base pair span settings after vrna_fold_compound_prepare()
• API: Return INF on predictions of vrna_mfe_dimer() that fail due to unsatisfiable constraints
• API: Rename internally used hard and soft constraints API symbols
• API: Fix header file inclusions to prevent #include cycles
• SWIG: Add wrapper for vrna_file_fasta_read_record()
• SWIG: Fix memory leak in wrapper for vrna_probs_window()
• SWIG: Refactor and therefore fix soft constraint binding functions for use in comparative structure predictions
• SWIG: Fix typo that prevented properly wrapping vrna_params_load_RNA_Andronescu2007()
• SWIG: Unify wrappers for vrna_ptable() and vrna_ptable_from_string()

• REFMAN: Refactored structure annotation documentation
• REFMAN: Update Mac OS X install section
• Replace DEF placeholders in energy parameter files with their value of -50
• Update RNAlocmin subpackage to properly compile with more stringent C++ compilers
• Update RNAforester subpackage to properly compile with more stringent C++ compilers
• Update autotools framework, e.g. checks for pthreads
• Update universal binary build instructions for Mac OS X builds to enable ARM compilation for M1 CPUs

• Fix RNAup -b mode with shorter sequence first
• Add --backtrack-global option to RNALfold (currently only available for dangles == 2 | 0)
• Add --zscore-pre-filter and --zscore-report-subsumed options to RNALfold

• API: Fix multiloop backtracing with soft constraints for unpaired positions in vrna_subopt() and vrna_subopt_cb()
• API: Fix parameter parse in vrna_params_load_from_string()
• API: Add vrna_heat_capacity() and vrna_head_capacity_cb() functions to RNAlib
• API: Add backtracing function vrna_backtrack_window() for global MFE structure to sliding-window predictions
• API: Add SVG support for RNApuzzler structure layouts
• API: Make vrna_md_t argument to vrna_fold_compound() a constant pointer
• API: Remove missing symbols from header file ViennaRNA/params/default.h
• API: Refactor z-score threshold filter handling for sliding-window MFE prediction
• SWIG: Fix typo in interface functions to load DNA parameters
• SWIG: Add python-3.9 autoconf checks
• SWIG: Add vrna_head_capacity*() wrappers
• SWIG: Add access to raw energy parameters
• SWIG: Add alias and pair attribute to objects of type md
• SWIG: Add out/varout typemaps for 2-dimensional int-like arrays
• SWIG: Add all data fields to objects of type 'param' and 'exp_param'

• Fix Debian and Windows installer files

• Fix backtracing errors in RNALalifold for alignments with more than 32768 columns
• Fix backtracing errors in RNAalifold and RNALalifold for rare cases when two alignment columns may pair due to covariance score threshold but still yield infinite energies due to energy model
• Refactored manpages/help options for RNAplfold, RNAplot, RNApvmin, RNAsubopt, and RNAup

• API: Fix undefined behavior due to short int overflows when accessing alignment lengths with alignments larger than 32768 columns. This fixes occasional backtracing errors in RNALalifold and vrna_mfe_window()
• API: Fix adding pscore to base pairs that yield INF energy in comparative global and local MFE prediction
• API: Add vrna_convert_kcal_to_dcal() and vice-versa function for safely converting integer to float representations of energy values
• SWIG: Add a reasonable Python interface for objects of type vrna_path_t
• SWIG: Add a wrapper for vrna_seq_encode()

• Move units.h include file to ViennaRNA/utils/units.h

• Fix compilation of Kinfold with GCC 10
• Add --en-only flag to RNAsubopt to allow for sorting by energy only
• Prevent RNAcofold to process input with more than two strands
• Add cutpoint marker to dot-plots created with RNAcofold -a
• Update Kinfold to version 1.4

• API: Fix removal of strand delimiter in vrna_plot_dp_PS_list()
• API: Fix vrna_enumerate_necklaces()
• API: Fix bogus backtracing for co-folded structures in vrna_subopt() and vrna_subopt_cb()
• API: Fix storing co-folded structures for sorted output in vrna_subopt()
• API: Fix multibranch loop component hard constraints for multi-strand cases
• API: Prevent adding internal loop energy contributions to enclosed parts with energy=INF
• API: Adapt vrna_db_pack()/vrna_db_unpack() functions to produce comparable strings
• API: Add sorting modes VRNA_UNSORTED, VRNA_SORT_BY_ENERGY_LEXICOGRAPHIC_ASC, and VRNA_SORT_BY_ENERGY_ASC to vrna_subopt()
• API: Add vrna_strjoin() function
• API: Add missing case to external loop hard constraints
• API: Make hard constrains strand-aware
• SWIG: Fix invalid memory access when using MEA_from_plist() in Perl 5 or Python
• SWIG: Enable keyword argument features in Python interface of constructors for fold_compound, md, move, param, and exp_param objects
• SWIG: Enable autodoc feature for Python interface of constructors for fold_compound, md, and move objects
• SWIG: Enable toString conversion for Python interface for objects of type fold_compound, md, move, params, exp_params, and subopt_solution
• SWIG: Add (read-only) attributes type, length, strands, params, and exp_params to objects of type fold_compound
• SWIG: Make attributes of objects of type param and exp_param read-only
• Add array of strand nicks to EPS dot plot files instead of single cutpoint
• Draw separator line for each strand nick in EPS dot-plots
• Update libsvm to version 3.24

• Disable Link-Time-Optimization (LTO) for third-party programs linking against RNAlib using pkg-config
• TESTS: Fix results dir path for out-of-tree builds
• TESTS: Set default timeout for library tests to 20s

• Fix RNApvmin pertubation vector computation
• Add non-redundant sampling option to RNApvmin
• Add RNAdos program to compute density of states
• Add -P DNA convenience command line parameter to most programs to quickly load DNA parameters without any input file
• MAN: Add example section to man-page of RNAalifold

• API: Fix memory leak in vrna_path_gradient()
• API: Fix release of memory fir vrna_sequence_remove_all()
• API: Fix soft-constraints application in vrna_sc_minimize_pertubation() that prevented proper computation of the pertubation vector
• API: Add 5' and 3' neighbor nucleotide encoding arrays and name string to vrna_seq_t
• API: Add new data structure for multiple sequence alignments
• API: Add vrna_sequence_order_update() function
• API: Add non-redundant sampling mode to vrna_sc_minimize_pertubation() through passing negative sample-sizes
• API: Add v3.0 API functions for maximum expected accuracy (MEA) computation
• API: Include energy parameter sets into RNAlib and provide functions to load them at runtime
• API: Prepare sequence data in vrna_fold_compound_t with vrna_sequence_add()
• API: Use vrna_pbacktrack_num() instead of vrna_pbacktrack() in vrna_sc_minimize_pertubation() to speed-up sample generation
• Reduce use of global variable cut_point in RNAlib
• SWIG: Use importlib in favor of imp to determine Python 3 tag extension
• SWIG: Update various wrapper functions
• SWIG: Add wrappers for MEA computation with vrna_MEA() and vrna_MEA_from_plist
• SWIG: Add wrappers for vrna_pr_structure() and vrna_pr_energy()

• REFMAN: Fix LaTeX code in units.h that prevented proper compilation with pdflatex
• Add an R script to create 2D landscape plots from RNA2Dfold output
• Add gengetopt to configure-time requirements to build man-pages
• Add new energy parameter file rna_misc_special_hairpins.par with additional UV-melting derived parameters for Tri- and Tetra-loops
• Update RNA Tutorial
• Colorize final configure script message
• REFMAN: Always use pdflatex to compile reference manual and tutorial
• EXAMPLES: Add Python script that performs computations equivalent to RNAfold -p --MEA

• Fix centroid structure prediction for RNAcofold
• Fix --noLP option for RNALalifold

• API: Refactor and fix collision handling in vrna_hash_table_t
• API: Fix one access using wrong index for odd dangles in loops/external.c
• API: Add two missing MLbase contributions for MFE prediction in loops/multibranch.c
• API: Refactor multiloop MFE backtracking for odd dangles
• API: Add function vrna_backtrack5() to allow for MFE backtracking of sub-sequences starting at the 5'-end
• API: Reduce usage of global macro TURN by replacing it with min_loop_size field of vrna_md_t
• API: Add functions vrna_path_direct() and vrna_path_direct_ub() that may also return move lists instead of dot-bracket lists
• API: Add functions vrna_pt_pk_remove() and vrna_db_pk_remove() that remove pseudoknots from an input structure
• API: Fix invalid memory access for lonely pair mode (--noLP) in comparative sliding-window MFE prediction
• SWIG: Fix access to global variable pf_smooth and pf_smooth attribute in model_details object
• SWIG: Fix Python reference counting for Py_None in interfaces/findpath.i wrapper
• SWIG: Refactor reference counting for all Python2 and Python3 wrappers
• REFMAN: Larger updates and restructuring of reference manual

• Install example scripts and source code files, e.g. to $prefix/share/ViennaRNA/examples
• Properly pass GSL, PTHREADS, and MPFR flags to sub-projects
• Fix RNApuzzler header file installation
• SWIG: Include Python 3.7 and 3.8 in list of autoconf-probed python interpreters
• SWIG: Fix wrapper building for swig >= 4.0.0

• Add non-redundant stochastic backtracing option for RNAalifold
• Add --noDP option to suppress dot-plot output in RNAfold and RNAalifold
• Add RNApuzzler (4) and RNAturtle (3) secondary structure layout algorithm options to RNAfold and RNAplot
• Update help/man page of RNALfold
• Allow for multiple input files and parallel input processing in RNAheat

• API: Fix declaration of vrna_move_apply_db()
• API: Fix vrna_path() lexicographical ordering in gradient walks
• API: Enable non-redundant stochastic backtracing for comparative structure prediction
• API: Enable stochastic backtracing for circular comparative structure prediction
• API: Enable stochastic backtracing of subsequences (5' prefixes) for comparative structure prediction
• API: Add pf_smooth attribute to vrna_md_t data stucture to allow for disabling Boltzmann factor energy smoothing
• API: Add functions to allow for resuming non-redundant stochastic backtracing
• API: Add functions to retrieve multiple stochastically backtraced structures (list and callback variants)
• API: Add vrna_positional_entropy to compute vector of positional entropies
• API: Add RNApuzzler and RNAturtle secondary structure layout algorithm (Wiegreffe et al. 2018)
• API: Add v3.0 API for secondary structure layout/coordinate algorithms
• API: Add more helper/utility functions for vrna_move_t data structures
• API: Add callback-based neighborhood update function for (subsequent) vrna_move_t application
• API: Add abstract heap data structure available as <ViennaRNA/datastructures/heap.h>
• API: Refactor and speed-up gradient walk implementation available as vrna_path_gradient()
• API: Substitute vrna_file_PS_aln_sub() alignment plot function by vrna_file_PS_aln_slice() that actually slices out a sub-alignment
• API: Rename vrna_annotate_covar_struct() to vrna_annotate_covar_db() and add new function vrna_annotate_covar_db_extended() to support more bracket types
• API: Calling vrna_params_reset() now implies a call to vrna_exp_params_reset() as well
• API: Move landscape implementations into separate directory, thus headers should be included as <ViennaRNA/landscape/move.h>, <ViennaRNA/landscape/neighbor.h>, etc.
• Ensure proper rescaling of energy parameters upon temperature changes
• Refactor soft constraints implementation in stochastic backtracing
• SWIG: Wrap all non-redundant stochastic backtracing functions to scripting language interface(s)
• SWIG: Refactor stochastic backtracing interface(s)
• SWIG: Add proper constructor for objects of type vrna_ep_t
• SWIG: Sanitize alignment plot function interface(s)

• Update Ubuntu/Debian and OpenSUSE build instructions
• Reduce intra-package dependency on non-v3.0 API

• Add --commands option to RNAsubopt
• Add non-redundant Boltzmann sampling mode for RNAsubopt

• API: Fix wrong access to base pair soft constraints in equilibrium probability computations
• API: Fix behavior of vrna_nucleotide_encode() with lowercase characters in sequence
• API: Fix behavior of encode_char() with lowercase characters in sequence
• API: Fix forbidden GU pairs behavior in pscore computation for comparative folding
• API: Fix potential errors due to uninitialized next pointers in vrna_move_t of vrna_eval_move_shift_pt
• API: Add AVX 512 optimized version of MFE multibranch loop decomposition
• API: Add functions for CPU SIMD feature detection
• API: Add dispatcher to automatically delegate exterior-/multibranch loop MFE decomposition to supported SIMD optimized implementation
• API: Add function vrna_dist_mountain() to compute mountain distance between two structures
• API: Add function vrna_ensemble_defect() to compute ensemble defect given a target structure
• API: Add non-redundant Boltzmann sampling
• API: Change behavior of vrna_cstr_free() and vrna_cstr_close() to always flush output before unregistering the stream
• SWIG: Add interface for vrna_loopidx_from_ptable()

• Activate compilation for compile-time supported SIMD optimized implementations by default
• Replace --enable-sse configure script option with --disable-simd

• Fix wrong output filename for binary opening energies in RNAplfold
• Enable G-Quadruplex support for partition function computation in RNAalifold

• Fix broken SSE4.1 support for multibranch loop MFE computation that resulted in increased run times
• Fix redundant output issue in subopt backtracking with unusually high delta energies (>=INF)
• Restore default behavior of '|' symbol in dot-bracket hard constraint strings that got lost with version 2.2.0
• Add faster (cache-optimized) version of Nussinov Maximum Matching algorithm
• Change default linker- and loop length computations for G-Quadruplex predictions in comparative prediction modes
• Add hard constraints warning for base pairs that violate the min_loop_size of the model
• Update libsvm to version 3.23
• API: Add functions to set auxiliary grammar extension rules
• API: Replace upper-triangular hard constraints matrix with full matrix for cache-optimized access
• API: Add G-Quadruplex prediction support for comparative partition function
• API: Remove VRNA_GQUAD_MISMATCH_PENALTY and VRNA_GQUAD_MISMATCH_NUM_ALI macros
• SWIG: Fix invalid memory access in subopt() method of fold_compound object when writing to file
• SWIG: Add wrapper for Nussinov Maximum Matching algorithm

• Add -ftree-vectorize compile flag by default if supported

• Fix interactive mode behavior for multiple sequence alignment input in RNAalifold, RNALalifold
• Allow for Stockholm formatted multiple sequence alignment input in RNAeval and RNAplot
• Allow for multiple input files in RNAeval and RNAplot
• Allow for parallel processing of input batch jobs in RNAeval and RNAplot
• Add -g option to activate G-Quadruplex support in RNAheat
• Warn on unsatisfiable hard constraints from dot-bracket string input in RNAfold, RNAcofold, and RNAalifold

• Fix parameter order bug in vrna_path_findpath* functions that resulted in too large search widths
• Fix wrong application of base pair soft constraints in partition function computations
• Fix position ruler string in EPS alignment output files
• Fix MFE backtracking errors that might appear under specific hard constrained base pair patterns
• Refrain from reading anything other than #=GC SS_cons to retrieve structures when parsing Stockholm 1.0 format
• Complete soft constraints additions to Boltzmann sampling implementation for single sequences
• Allow for disabling alignment wrapping in vrna_file_PS_aln* functions
• Do not remove G-Quadruplex annotation from WUSS formatted structure strings upon calls to vrna_db_from_WUSS
• Enable G-Quadruplex related average loop energy correction terms in verbose output of vrna_eval_* functions
• Speed-up backward compatibility layer for energy evaluation functions that unnecessarily slowed down third-party tools using the old API
• Allow for passing dot-bracket strings with '&' strand-end identifier to simple vrna_eval_* functions
• Remove implicit exit() calls from global MFE backtracking implementation.

• Fix compilation of RNAforester with C++17 standard
• Fix tty input detection in RNAcofold
• Fix bad memory access with RNAcofold -p

• API: Fix incorrect unpaired probability computations in vrna_probs_window()
• API: Fix potential out-of-bounds access situations (for circular RNA folding) in eval.c
• API: Fix comparative exterior internal loop partition function computation for circfold
• SWIG: Fix false-positive use of uninitialized value in Python3/file_py3.i

• TESTS: Add tests for special features in RNAalifold
• TESTS: Add test case for RNAcofold -p

• Allow for parallel processing across multiple input files in RNAfold
• Allow for arbitrary number of input files in RNAalifold
• Allow for parallel processing of input data in RNAalifold
• Allow for arbitrary number of input files in RNAcofold
• Allow for parallel processing of input data in RNAcofold
• Enable parallel processing in RNAfold, RNAcofold, RNAalifold for MS Windows build
• Add centroid and MEA structure computation to RNAcofold
• Add configure time check for LTO capabilities of the linker
• Include ligand binding energies in centroid and MEA structure output of RNAfold
• Refactor ct2db program to process multiple structures from single .ct file
• API: Enable processing of comparative fold_compound with vrna_pr_*() functions
• API: Refactor vrna_ostream_t to enable NULL input in vrna_ostream_provide()
• API: Major refactoring in loop energy evaluations (MFE and PF)
• API: Make vrna_mx_pf_aux_el_t and vrna_mx_pf_aux_ml_s opaque pointers
• API: Make fold_compound field type a const attribute
• API: Refactor MFE post-processing for circular RNAs
• API: Add motif name/id support for unstructured domains
• API: Remove major part of implicit exit() calls in RNAlib
• API: Add implementations of Boyer-Moore-Horspool search algorithm
• API: Add implementations to determine number of rotational symmetry for strings (of objects)
• API: Make vrna_cmd_t an opaque pointer
• API: Move headers for constraints, datastructures, io, loop energy evaluation, energy parameters, plotting, search, and utilities into separate subdirectories (backward compatibility is maintained)
• API: Add hash table data structure
• API: Fix discrepancy between comparative and single sequence --noLP predictions
• API: Add functions to replace 'old API' interface of RNAstruct.h
• API: Add functions to replace 'old API' interface of aln_util.h
• API: Add generic soft constraints support to suboptimal structure prediction sensu Wuchty et al.
• SWIG: Refactor callback execution for Python 2 / 3 interface to reduce overhead
• SWIG: Fix configure-time check for Python 3 interface build
• SWIG: Fix Python 3 IO file stream to C FILE * conversion
• Cosmetic changes in final configure notice
• Major changes in source tree structure of the library
• Add autoconf checks for maintainer tools
• Generate C strings from static PostScript files at configure time (for structure- and dot plots)
• REFMAN: Large updates in API documentation and structure of reference manual

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• Fix multiloop contributions for comparative partition function
• Fix building python2 extension module for OSX

• 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

• 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)

• 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

• 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

• 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

• 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

• 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

• 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

• 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

• Fixed bug in RNAsubopt that occasionally produced cofolded structures twice
• Removed debugging output in preparations of consensus structure prediction datastructures

• 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()

• Fix regression bug that occasionally prevented backtracking with RNAcofold --noLP

• 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

• 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

• 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

• 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

• 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

• 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)

• Fix for discrepancy between special hairpin loop evaluation in partition functions and MFE

• Fix of G-quadruplex support in subopt()
• Fix for discrepancy between special hairpin loop evaluation in partition functions and MFE

• 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()

• 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.

• Bugfix to restore backward compatibility with ViennaRNA Package 1.8.x API (this bug also affected proper usage of the the perl interface)

• 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

• Bugfix for RNAplfold where segfault happened upon usage of -O option
• Corrected misbehavior of RNAeval and RNAplot in tty mode

• 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

• Restored z-score computation capabilities in RNALfold

• Bugfix for RNAcofold partition function
• Perl wrapper compatibility to changed RNAlib has been restored
• Backward compatibility for partition function calls has been restored

• 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.

• added support for Boltzmann factor scaling in RNAfold
• fixed fastaheader to filename bug
• plugged some memory leaks

• First official release of version 2.0
• included latest bugfixes

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

• Fix memory corruption in PS_color_aln()

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

• add a loop_energy() function to compute energy of a single loop

2007-06-23 Ivo Hofacker ivo@tbi.univie.ac.at

• add aliLfold() and RNALalifold, alignment variant of Lfold()

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

• add circular folding in alifold()

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

• update RNAplfold to working version
• add PS_dot_plot_turn() in PS_dot.c

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

• adapt PS_rna_plot() for drawing co-folded structures

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

• move alifold() into the library

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

• change Make_bp_profile() and profile_edit_distance() to use simple (float *) arrays; makes Perl access much easier. RNApdist -B now works again

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

• added co-folding support in energy_of_struct(), and thus RNAeval

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