New upstream version 2.4.6+dfsg

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

 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/

pkgconfig_DATA = RNAlib2.pc

EXTRA_DIST =  INSTALL.configure \

              examples

              examples \

              packaging/debian \

              packaging/make_windows_installer.sh \

              license.txt

# 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,

	$(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 \

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@

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@

am__quote = @am__quote@

am__tar = @am__tar@

am__untar = @am__untar@

ax_pthread_config = @ax_pthread_config@

bibtex = @bibtex@

bindir = @bindir@

build = @build@

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

[![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. 

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

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

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