ChangeLog

+v2.4.6
+  * Stabilize rounding of free energy output in RNAalifold
+  * API: Fix potential rounding errors for comparative free energies in eval.c and mfe.c
+  * API: Fix regression in exterior loop dangling end contributions for comparative base pair probabilities and Boltzmann sampling (introduced with v2.4.4)
+  * API: Fix regression with hard constrained base pairs for comparative structure prediction (introduced with v2.4.4)
+  * TESTS: Add basic tests for RNAalifold executable
+  * TESTS: Ignore 'frequency of MFE structure' in RNAcofold partition function checks
+
+
+v2.4.5
+  * Allow for arbitrary number of input files in RNAfold
+  * Allow for parallel processing of input data in RNAfold (UNIX only, no Windows support yet)
+  * Add SHAPE reactivity support through commandline options for RNAplfold
+  * Fix unstructured domain motif detection in MFE, centroid, and MEA structures computed by RNAfold
+  * Limit allowed set of commands in command file for RNAcofold to hard and soft constraints
+  * API: Add functions to compute equilibrium probability of particular secondary structures
+  * API: Add dynamic string stream data type and associated functions
+  * API: Add priority-queue like data structure with unordered fill capability and ordered output callback execution
+  * API: Add functions to detect unstructured domain motifs in MFE, centroid, and MEA structures
+  * API: Fix bug in sliding-window partition function computation with SHAPE reactivity and Deigan et al. conversion method
+  * API: Fix application of '<' and '>' constraint symbols in dot-bracket provided constraints (was broken since v2.4.2)
+  * API: Fix MEA structure computation in the presence of unstructured domains
+  * API: Stabilize order of probability entries in EPS dot-plot files
+  * Fix compiler warnings on wrong type of printf() in naview.c
+  * Define VRNA_VERSION macro as string literal and add macros for major, minor, and patch numbers
+  * Stabilize parallel make of Mac OS X installer
+  * Add energy parameter set from Langdon et al. 2018
+  * Add autoconf checks for POSIX threads compiler/linker support
+  * SWIG: Fix 'next' is a perl keyword warnings for Perl5 wrapper
+  * SWIG: Catch errors and throw execptions whenever scripting language provided callback functions are not applicable or fail
+  * SWIG: Add keyword arguments and autodoc feature for Python/Python3 wrappers
+
+
+v2.4.4
+  * Change verbose output for soft-constraints derived ligand binding motifs in RNAfold
+  * Allow for lowercase letters in ct2db input
+  * Fix bug in interior-like G-Quadruplex MFE computation for single sequences
+  * Fix autoconf switch to enable deprecation warnings
+  * Fix bug in eval_int_loop() that prevented propagation of energy evaluation for loops with nick in strands
+  * Fix several bugs for SHAPE reactivity related comparative partition function computations
+  * Fix annotation of PostScript output for soft-constraint derived ligand binding motifs in RNAfold
+  * Fix constraint indices for multibranch loops in unpaired probability computations of LPfold.c
+  * Fix dangling end contributions in comparative partition function for exterior loops
+  * API: Add simplified interface for vrna_pf_dimer()
+  * API: Move concentraton dependent implementation for co-folding to separate compile unit
+  * API: Add new API functions for exterior loop evaluations
+  * API: Add simplified interfaces for energy evaluation with G-Quadruplexes and circular RNAs
+  * API: Add findpath functions that allow for specification of an upper bound for the saddle point
+  * Add configure-time linker check for Python3 interface
+  * Add automatic CPP suggestions for deprecated function substitutes
+  * Major restucturing and constraints feature additions in loop type dependent energy evaluation functions
+  * Major restructuring in MFE implementations
+  * Major restructuring in PF implementations
+  * Minor fixes in Boltzmann sampling implementation
+  * SWIG: Fix wrappers for findpath() implementation
+  * SWIG: Add tons of energy evaluation wrappers
+  * SWIG: Fix configure-time check of Perl5 interface build capabilities
+  * SWIG: Wrap functions from walk.c and neighbor.c
+  * DOC: Add some missing references to manpages of executable programs
+  * REFMAN: Heavy re-ordering of the RNAlib reference manual
+
+
 v2.4.3
   * Fix handling of dangling end contribution at sequence boundaries for sliding window base pair probability computations
   * Fix handling of base pair hard constraints in sliding-window implementations

INSTALL

@@ -64,12 +64,8 @@ Memory requirements for a sequence of length n will be approximately
  4*n^2 bytes for the minimum free energy alone.
   
 
-The readseq program is not integrated in the build process. If desired,
-install readseq manually, following the instructions in the readseq
-directory.
-
 There are man pages for all executables, the library is documented in
-./doc/RNAlib-2.3.3.pdf as well as a set of HTML pages in
+./doc/RNAlib-2.4.6.pdf as well as a set of HTML pages in
 ./doc/html/index.html. Documentation in HTML can also be found at
 http://www.tbi.univie.ac.at/RNA/
 

Makefile.am

@@ -10,4 +10,7 @@ pkgconfigdir = $(libdir)/pkgconfig
 pkgconfig_DATA = RNAlib2.pc
 
 EXTRA_DIST =  INSTALL.configure \
-              examples
+              examples \
+              packaging/debian \
+              packaging/make_windows_installer.sh \
+              license.txt

Makefile.in

-# Makefile.in generated by automake 1.15.1 from Makefile.am.
+# Makefile.in generated by automake 1.15 from Makefile.am.
 # @configure_input@
 
-# Copyright (C) 1994-2017 Free Software Foundation, Inc.
+# Copyright (C) 1994-2014 Free Software Foundation, Inc.
 
 # This Makefile.in is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -106,7 +106,7 @@ am__aclocal_m4_deps = $(top_srcdir)/m4/ac_rna.m4 \
 	$(top_srcdir)/m4/ax_compiler_vendor.m4 \
 	$(top_srcdir)/m4/ax_openmp.m4 $(top_srcdir)/m4/ax_perl_ext.m4 \
 	$(top_srcdir)/m4/ax_perl_ext_flags.m4 \
-	$(top_srcdir)/m4/ax_pkg_swig.m4 \
+	$(top_srcdir)/m4/ax_pkg_swig.m4 $(top_srcdir)/m4/ax_pthread.m4 \
 	$(top_srcdir)/m4/ax_python2_devel.m4 \
 	$(top_srcdir)/m4/ax_python3_devel.m4 \
 	$(top_srcdir)/m4/ax_require_defined.m4 \
@@ -413,6 +413,9 @@ PKG_CONFIG_LIBDIR = @PKG_CONFIG_LIBDIR@
 PKG_CONFIG_PATH = @PKG_CONFIG_PATH@
 POW_LIB = @POW_LIB@
 PRODUCTBUILD = @PRODUCTBUILD@
+PTHREAD_CC = @PTHREAD_CC@
+PTHREAD_CFLAGS = @PTHREAD_CFLAGS@
+PTHREAD_LIBS = @PTHREAD_LIBS@
 PYEXEC2DIR = @PYEXEC2DIR@
 PYTHON2 = @PYTHON2@
 PYTHON2DIR = @PYTHON2DIR@
@@ -467,6 +470,9 @@ USER_RANLIB = @USER_RANLIB@
 VERSION = @VERSION@
 VRNA_CFLAGS = @VRNA_CFLAGS@
 VRNA_LIBS = @VRNA_LIBS@
+VRNA_VERSION_MAJOR = @VRNA_VERSION_MAJOR@
+VRNA_VERSION_MINOR = @VRNA_VERSION_MINOR@
+VRNA_VERSION_PATCH = @VRNA_VERSION_PATCH@
 _latex_cmd = @_latex_cmd@
 abs_builddir = @abs_builddir@
 abs_srcdir = @abs_srcdir@
@@ -481,6 +487,7 @@ am__leading_dot = @am__leading_dot@
 am__quote = @am__quote@
 am__tar = @am__tar@
 am__untar = @am__untar@
+ax_pthread_config = @ax_pthread_config@
 bibtex = @bibtex@
 bindir = @bindir@
 build = @build@
@@ -543,7 +550,10 @@ SUBDIRS = src man misc doc RNA-Tutorial interfaces @subdirs@ tests packaging/mac
 pkgconfigdir = $(libdir)/pkgconfig
 pkgconfig_DATA = RNAlib2.pc
 EXTRA_DIST = INSTALL.configure \
-              examples
+              examples \
+              packaging/debian \
+              packaging/make_windows_installer.sh \
+              license.txt
 
 all: config.h
 	$(MAKE) $(AM_MAKEFLAGS) all-recursive

README

 [![Build Status](https://travis-ci.org/ViennaRNA/ViennaRNA.svg?branch=master)](https://travis-ci.org/ViennaRNA/ViennaRNA)
 
-This is Version 2.4.3 of the ViennaRNA Package.
-------------------------------------------------
-See the NEWS and Changelog files for differences to previous versions.
+# ViennaRNA Package
+
+## Version 2.4.6
+
+See the [NEWS](NEWS) and [ChangeLog](ChangeLog) files for changes between versions.
+
+## About
 
 The ViennaRNA Package consists of a few stand alone programs and a 
 library that you can link your own programs with. 
@@ -36,17 +40,34 @@ There is also a set of programs for analyzing sequence and distance
 data using split decomposition, statistical geometry, and cluster methods.
 They are not maintained any more and not built by default.
 
-See the NEWS and Changelog files for changes between versions.
+The code very rarely uses static arrays, and all programs should work for 
+sequences up to a length of 32,700 (if you have huge amounts of memory that
+is).
+
+## Copyright
 
-Please read the copyright notice in the file COPYING!
+Please read the copyright notice in the file [COPYING](COPYING)!
+
+If you're a commercial user and find these programs useful, please consider
+supporting further developments with a donation.
+
+## Availability
+
+The most recent source code and documentation should always be available through
+the [official ViennaRNA website](https://www.tbi.univie.ac.at/RNA) and through
+[github](https://github.com/ViennaRNA/ViennaRNA).
+
+## Compatibility
 
 The package should be easily portable. It is known to compile without
 modifications at least under
-SunOS 5.x, IRIX 5.x and 6.x, linux, and MS Windows with the Cygwin environment.
+SunOS 5.x, IRIX 5.x and 6.x, Linux, and MS Windows with the Cygwin environment.
 Other UNIX flavors should present no problems.
-You need a compiler that understands ANSI C. See the INSTALL file for details.
+You need a compiler that understands ANSI C. See the [INSTALL](INSTALL) file for details.
+
+## Executable Programs
 
-The following executables are provided:
+The following executable programs are provided:
 - `RNA2Dfold`       Compute MFE structure, partition function and representative sample structures of k,l neighborhoods
 - `RNAaliduplex`    Predict conserved RNA-RNA interactions between two alignments
 - `RNAalifold`      Calculate secondary structures for a set of aligned RNA sequences
@@ -80,10 +101,31 @@ switches rather than menus to be easily usable in pipes.
 
 For more detailed information see the man pages. Perl utilities contain
 POD documentation that can be read by typing e.g.
+```
 perldoc relplot.pl
+```
+
+## References
 
-Since version 2.0 the build-in energy parameters (available as parameter
-file default.par as well) are taken from:
+If you use our software package, you may want to cite
+
+[R. Lorenz et al. (2004)](https://almob.biomedcentral.com/articles/10.1186/1748-7188-6-26),
+"ViennaRNA Package 2.0", Algorithms for Molecular Biology, 6:26
+
+and
+
+[I.L. Hofacker (1994)](https://link.springer.com/article/10.1007/BF00818163),
+"Fast folding and comparison of RNA secondary structures",
+Monatshefte fuer Chemie, Volume 125, Issue 2, pp 167-188
+
+
+*Note, that the individual executable programs state their own list of references
+in the corresponding man-pages.*
+
+### Energy Parameters
+
+Since version 2.0 the build-in energy parameters, also available as parameter
+file [rna_turner2004.par](misc/rna_turner2004.par), are taken from:
 
 [D.H. Mathews et al. (2004)](https://doi.org/10.1073/pnas.0401799101),
 "Incorporating chemical modification constraints into a dynamic programming
@@ -98,23 +140,18 @@ for predicting stability of nucleic acid secondary structure",
 Nucleic Acids Research: 38, pp 280-282.
 
 For backward compatibility we also provide energy parameters from Turner et al.
-1999 in the file 'rna_turner1999.par'. Additionally, a set of trained RNA energy
-parameters from Andronescou et al. 2007 'rna_andronescou2007.par' and two sets
-of DNA parameters ('dna_mathews1999.par' and 'dna_mathews2004.par') are included
+1999 in the file [rna_turner1999.par](misc/rna_turner1999.par). Additionally,
+a set of trained RNA energy parameters from Andronescou et al. 2007,
+[rna_andronescou2007.par](misc/rna_andronescou2007.par), a set of RNA energy
+parameters obtained by graft and grow genetic programming from Langdon
+et al. 2018, [rna_langdon2018.par](misc/rna_langdon2018.par), and two sets
+of DNA parameters, [dna_mathews1999.par](misc/dna_mathews1999.par) and
+[dna_mathews2004.par](misc/dna_mathews2004.par), are included
 in the package as well.
-The code very rarely uses static arrays, and all programs should work for 
-sequences up to a length of 32,700 (if you have huge amounts of memory that
-is).
 
-If you're a commercial user and find these programs useful, please consider
-supporting further developments with a donation.
-
-The most recent source code and documentation should always be available on
-the web at 
-[http://www.tbi.univie.ac.at/RNA](http://www.tbi.univie.ac.at/RNA)
+## Contact
 
 We need your feedback! Send your comments, suggestions, and questions to
 rna@tbi.univie.ac.at
 
 Ivo Hofacker, Spring 2006
-