# Changelog

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

## Version 2.6.x

### [Unreleased](https://github.com/ViennaRNA/ViennaRNA/compare/v2.6.4...HEAD)


### [Version 2.6.4](https://github.com/ViennaRNA/ViennaRNA/compare/v2.6.3...v2.6.4)

#### Programs
  * 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

#### Library
  * 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`

#### Package
  * 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


### [Version 2.6.3](https://github.com/ViennaRNA/ViennaRNA/compare/v2.6.2...v2.6.3)

#### Library
  * 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)

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


### [Version 2.6.2](https://github.com/ViennaRNA/ViennaRNA/compare/v2.6.1...v2.6.2) (Release date: 2023-06-21)

#### Programs
  * Fix preparation of input sequences for modified base support in `RNAcofold`

#### Library
  * 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

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


### [Version 2.6.1](https://github.com/ViennaRNA/ViennaRNA/compare/v2.6.0...v2.6.1) (Release date: 2023-06-12)

#### Programs
  * 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

#### Package
  * AUTOCONF: Update autoconf macros
  * Update Debian-based packaging rules

### [Version 2.6.0](https://github.com/ViennaRNA/ViennaRNA/compare/v2.5.1...v2.6.0) (Release date: 2023-06-09)

#### Programs
  * 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

#### Library
  * 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

#### Package
  * 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


## Version 2.5.x

### [Version 2.5.1](https://github.com/ViennaRNA/ViennaRNA/compare/v2.5.0...v2.5.1) (Release date: 2022-06-02)

#### Programs
  * Refactor `ct2db` program to allow for pseudoknots in output structure

#### Library
  * 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()`

#### Package
  * 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

### [Version 2.5.0](https://github.com/ViennaRNA/ViennaRNA/compare/v2.4.18...v2.5.0) (Release date: 2021-11-08)

#### Programs
  * 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`

#### Library
  * 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()`

#### Package
  * 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/`


## Version 2.4.x

### [Version 2.4.18](https://github.com/ViennaRNA/ViennaRNA/compare/v2.4.17...v2.4.18) (Release date: 2021-04-22)

#### Programs
  * 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 

#### Library
  * 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()`

#### Package
  * 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

### [Version 2.4.17](https://github.com/ViennaRNA/ViennaRNA/compare/v2.4.16...v2.4.17) (Release date: 2020-11-25)

#### Programs
  * 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`

#### Library
  * 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'

#### Package
  * Fix Debian and Windows installer files


### [Version 2.4.16](https://github.com/ViennaRNA/ViennaRNA/compare/v2.4.15...v2.4.16) (Release date: 2020-10-09)

#### Programs
  * 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`

#### Library
  * 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()`

#### Package
  * Move `units.h` include file to `ViennaRNA/utils/units.h`


### [Version 2.4.15](https://github.com/ViennaRNA/ViennaRNA/compare/v2.4.14...v2.4.15) (Release date: 2020-08-18)

#### Programs
  * 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`

#### Library
  * 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

#### Package
  * 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


### [Version 2.4.14](https://github.com/ViennaRNA/ViennaRNA/compare/v2.4.13...v2.4.14) (Release date: 2019-08-13)

#### Programs
  * 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`

#### Library
  * 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()`

#### Package
  * 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`


### [Version 2.4.13](https://github.com/ViennaRNA/ViennaRNA/compare/v2.4.12...v2.4.13) (Release date: 2019-05-30)

#### Programs
  * Fix centroid structure prediction for `RNAcofold`
  * Fix `--noLP` option for `RNALalifold`

#### Library
  * 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

#### Package
  * 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`


### [Version 2.4.12](https://github.com/ViennaRNA/ViennaRNA/compare/v2.4.11...v2.4.12) (Release date: 2019-04-16)

#### Programs
  * 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`

#### Library
  * 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)

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


### [Version 2.4.11](https://github.com/ViennaRNA/ViennaRNA/compare/v2.4.10...v2.4.11) (Release date: 2018-12-17)

#### Programs
  * Add `--commands` option to `RNAsubopt`
  * Add non-redundant Boltzmann sampling mode for `RNAsubopt`

#### Library
  * 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()`

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


### [Version 2.4.10](https://github.com/ViennaRNA/ViennaRNA/compare/v2.4.9...v2.4.10) (Release date: 2018-09-26)

#### Programs
  * Fix wrong output filename for binary opening energies in `RNAplfold`
  * Enable G-Quadruplex support for partition function computation in `RNAalifold`

#### Library
  * 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

#### Package
  * Add `-ftree-vectorize` compile flag by default if supported


### [Version 2.4.9](https://github.com/ViennaRNA/ViennaRNA/compare/v2.4.8...v2.4.9) (Release date: 2018-07-11)

#### Programs
  * 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`

#### Library
  * 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.


### [Version 2.4.8](https://github.com/ViennaRNA/ViennaRNA/compare/v2.4.7...v2.4.8) (Release date: 2018-06-23)

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

#### Library
  * 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

#### Package
  * TESTS: Add tests for special features in RNAalifold
  * TESTS: Add test case for RNAcofold -p


### [Version 2.4.7](https://github.com/ViennaRNA/ViennaRNA/compare/v2.4.6...v2.4.7) (Release date: 2018-06-13)
  * 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


### [Version 2.4.6](https://github.com/ViennaRNA/ViennaRNA/compare/v2.4.5...v2.4.6) (Release date: 2018-04-19)
  * 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


### [Version 2.4.5](https://github.com/ViennaRNA/ViennaRNA/compare/v2.4.4...v2.4.5) (Release date: 2018-04-17)
  * 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


### [Version 2.4.4](https://github.com/ViennaRNA/ViennaRNA/compare/v2.4.3...v2.4.4) (Release date: 2018-03-06)
  * 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


### [Version 2.4.3](https://github.com/ViennaRNA/ViennaRNA/compare/v2.4.2...v2.4.3) (Release date: 2017-11-14)
  * 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


### [Version 2.4.2](https://github.com/ViennaRNA/ViennaRNA/compare/v2.4.1...v2.4.2) (Release date: 2017-10-13)
  * 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


### [Version 2.4.1](https://github.com/ViennaRNA/ViennaRNA/compare/v2.4.0...v2.4.1) (Release date: 2017-08-23)
  * 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


### [Version 2.4.0](https://github.com/ViennaRNA/ViennaRNA/compare/v2.3.5...v2.4.0) (Release date: 2017-08-01)
  * 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


## Version 2.3.x

### [Version 2.3.5](https://github.com/ViennaRNA/ViennaRNA/compare/v2.3.4...v2.3.5) (Release date: 2017-04-14)
  * 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


### [Version 2.3.4](https://github.com/ViennaRNA/ViennaRNA/compare/v2.3.3...v2.3.4) (Release date: 2017-03-10)
  * 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


### [Version 2.3.3](https://github.com/ViennaRNA/ViennaRNA/compare/v2.3.2...v2.3.3) (Release date: 2017-01-24)
  * Fix multiloop contributions for comparative partition function
  * Fix building python2 extension module for OSX


### [Version 2.3.2](https://github.com/ViennaRNA/ViennaRNA/compare/v2.3.1...v2.3.2) (Release date: 2017-01-18)
  * 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


### [Version 2.3.1](https://github.com/ViennaRNA/ViennaRNA/compare/v2.3.0...v2.3.1) (Release date: 2016-11-15)
  * 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)


### [Version 2.3.0](https://github.com/ViennaRNA/ViennaRNA/compare/v2.2.10...v2.3.0) (Release date: 2016-11-01)
  * 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


## Version 2.2.x

### [Version 2.2.10](https://github.com/ViennaRNA/ViennaRNA/compare/v2.2.9...v2.2.10) (Release date: 2016-09-06)
  * 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


### [Version 2.2.9](https://github.com/ViennaRNA/ViennaRNA/compare/v2.2.8...v2.2.9) (Release date: 2016-09-01)
  * 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


### [Version 2.2.8](https://github.com/ViennaRNA/ViennaRNA/compare/v2.2.7...v2.2.8) (Release date: 2016-08-01)
  * 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


### [Version 2.2.7](https://github.com/ViennaRNA/ViennaRNA/compare/v2.2.6...v2.2.7) (Release date: 2016-06-30)
  * 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


### [Version 2.2.6](https://github.com/ViennaRNA/ViennaRNA/compare/v2.2.5...v2.2.6) (Release date: 2016-06-19)
  * 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


### [Version 2.2.5](https://github.com/ViennaRNA/ViennaRNA/compare/v2.2.4...v2.2.5) (Release date: 2016-04-09)
  * 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


### [Version 2.2.4](https://github.com/ViennaRNA/ViennaRNA/compare/v2.2.3...v2.2.4) (Release date: 2016-02-19)
  * Fixed bug in RNAsubopt that occasionally produced cofolded structures twice
  * Removed debugging output in preparations of consensus structure prediction datastructures


### [Version 2.2.3](https://github.com/ViennaRNA/ViennaRNA/compare/v2.2.2...v2.2.3) (Release date: 2016-02-13)
  * 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()


### [Version 2.2.2](https://github.com/ViennaRNA/ViennaRNA/compare/v2.2.1...v2.2.2) (Release date: 2016-02-08)
  * Fix regression bug that occasionally prevented backtracking with RNAcofold --noLP


### [Version 2.2.1](https://github.com/ViennaRNA/ViennaRNA/compare/v2.2.0...v2.2.1) (Release date: 2016-02-06)
  * 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


### [Version 2.2.0](https://github.com/ViennaRNA/ViennaRNA/compare/v2.1.9...v2.2.0) (Release date: 2016-01-25)
  * 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


## Version 2.1.x

### [Version 2.1.9](https://github.com/ViennaRNA/ViennaRNA/compare/v2.1.8...v2.1.9)
  * 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


### [Version 2.1.8](https://github.com/ViennaRNA/ViennaRNA/compare/v2.1.7...v2.1.8)
  * 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


### [Version 2.1.7](https://github.com/ViennaRNA/ViennaRNA/compare/v2.1.6...v2.1.7)
  * 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


### [Version 2.1.6](https://github.com/ViennaRNA/ViennaRNA/compare/v2.1.5...v2.1.6)
  * 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)


### [Version 2.1.5](https://github.com/ViennaRNA/ViennaRNA/compare/v2.1.4...v2.1.5)
  * Fix for discrepancy between special hairpin loop evaluation in partition functions and MFE


### [Version 2.1.4](https://github.com/ViennaRNA/ViennaRNA/compare/v2.1.3...v2.1.4)
  * Fix of G-quadruplex support in subopt()
  * Fix for discrepancy between special hairpin loop evaluation in partition functions and MFE


### [Version 2.1.3](https://github.com/ViennaRNA/ViennaRNA/compare/v2.1.2...v2.1.3)
  * 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()


### [Version 2.1.2](https://github.com/ViennaRNA/ViennaRNA/compare/v2.1.1...v2.1.2)
  * 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. 


### [Version 2.1.1](https://github.com/ViennaRNA/ViennaRNA/compare/v2.1.0...v2.1.1)
  * Bugfix to restore backward compatibility with ViennaRNA Package 1.8.x API (this bug also affected proper usage of the the perl interface)


### [Version 2.1.0](https://github.com/ViennaRNA/ViennaRNA/compare/v2.0.7...v2.1.0)
  * 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


## Version 2.0.x

### [Version 2.0.7](https://github.com/ViennaRNA/ViennaRNA/compare/v2.0.6...v2.0.7)
  * Bugfix for RNAplfold where segfault happened upon usage of -O option
  * Corrected misbehavior of RNAeval and RNAplot in tty mode


### [Version 2.0.6](https://github.com/ViennaRNA/ViennaRNA/compare/v2.0.5...v2.0.6)
  * 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


### [Version 2.0.5](https://github.com/ViennaRNA/ViennaRNA/compare/v2.0.4...v2.0.5)
  * Restored z-score computation capabilities in RNALfold


### [Version 2.0.4](https://github.com/ViennaRNA/ViennaRNA/compare/v2.0.3...v2.0.4)
  * Bugfix for RNAcofold partition function
  * Perl wrapper compatibility to changed RNAlib has been restored
  * Backward compatibility for partition function calls has been restored 


### [Version 2.0.3](https://github.com/ViennaRNA/ViennaRNA/compare/v2.0.2...v2.0.3)
  * 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.


### [Version 2.0.2](https://github.com/ViennaRNA/ViennaRNA/compare/v2.0.1...v2.0.2)
  * added support for Boltzmann factor scaling in RNAfold
  * fixed fastaheader to filename bug
  * plugged some memory leaks


### Version 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>

  * 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
