Viennarna

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This version introduces modified nucleotides support and a physics-based model to
correct for predictions at non-standard (monovalent) salt concentrations.
At this time we include publically available energy parameters for inosine,
pseudouridine, m6A, 7DA, and purine (a.k.a. nebularine). In addition, we add
stacking parameters for dihydrouridine as predicted by Rosetta/RECESS.

See the Changelog for version 2.6.0 for a complete list of new features and bugfixes.

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The all new release of version 2.5 brings multi-strand interaction prediction! The
new executable tool RNAmultifold is the successor of the RNA-RNA dimer interaction
prediction tool RNAcofold and effectively lifts the restriction to just two interacting
strands. It follows the same principle of concatenating the RNA strands that shall
form a complex and then predicts MFE and partition function. Along with that, it can
also compute equilibrium concentrations of the complexes formed.

See the Changelog for version 2.5.0 for a complete list of additions, novel features
and fixed bugs.

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With version 2.4 sliding-window structure prediction receives the constraint framework!
Starting with this version, the sliding-window secondary structure prediction implementations
as available through RNALfold, RNAplfold, and RNALalifold are constraints-aware. Thus, they
can readily incorporate RNA structure probing data, such as from SHAPE experiments, etc.

See the Changelog for version 2.4.0 for a complete list of new features and bugfixes.

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This version introduces the unstructured domain extension of the RNA folding grammar! This
extension adds RNA-ligand interactions, e.g. RNA-protein, for unpaired stretches in RNA
secondary structures. The feature is easy to use through the command file interface in RNAfold.

See the Changelog for version 2.3.0 for a complete list of new features and bugfixes.

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After almost a year without a new release, we are happy to announce many new features. This
version officially introduces (generic) hard- and soft-constraints for many of the folding
algorithms. Thus, chemical probing constraints, such as derived from SHAPE experiments, can
be easily incorporated into RNAfold, RNAalifold, and RNAsubopt. Furthermore, RNAfold and the
RNAlib interface allow for a simple way to incorporate ligand binding to specific hairpin- or
interior-loop motifs. This version also introduces the new v3.0 API of the RNAlib C-library,
that will eventually replace the current interface in the future.

See the Changelog for version 2.2.0 for a complete list of new features and bugfixes.

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This is a major bugfix release that changes the way how the ViennaRNA Package handles
dangling end and terminal mismatch contributions for exterior-, and multibranch loops. We strongly
recommend upgrading your installation to this or a newer version to obtain predictions that are
better comparable to RNAstructure or UNAFold.

Please see the Changelog for version 2.1.9 for further details on the actual changes to the
underlying energy parameters.