Viennarna

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For a long time, Mac OS X users were not able to correctly build the Perl/Python interface of the
ViennaRNA Package. Starting with v2.1.7, this limitation has been removed, and the interface should
compile and work as expected.

Please see the Install Notes for Mac OS X users for further details.

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Since ViennaRNA Package Version 2.1.0 we have enabled G-Quadruplex prediction support into
RNAfold, RNAcofold, RNALfold, RNAalifold, RNAeval and RNAplot.

See the changelog for details.


Older news

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- Meanwhile, a lot of changes in the RNAlib have accumulated. See the Reference
Manual and the Changelog for further details
- All algorithms use the Turner'04 nearest neighbor model
- The RNAlib provides (OpenMP) threadsafe folding routines per default. This is
enables concurrent calls to the folding routines in parallel. The feature
can be disabled by passing '--disable-openmp' to the configure script
- serious changes in command line parameters. Everything complies with
GNU standard from now on (short options with preceding '-', long options
with preceding '--'.
- FASTA file support for RNAfold. RNA sequences do not need to be passed
on a single line anymore when a FASTA header is provided.
- The new program RNA2Dfold computes MFE, partition function and
stochastically sampled secondary structures in a partitioning of the secondary
structure space according to the base pair distance to two reference structures
- The new program PKplex computes...
- The new program RNALfoldz computes locally stable secondary structures
together with a z-score
- The new program RNALalifold computes locally stable consensus structures for
alignments
- The new program RNAparconv enables the conversion of 'old' energy parameter files
(v1.4-v1.8) to the new format used in version 2.x

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- new RNAalifold has better treatment of gaps and ribosum based covariance
scores. Use the -old switch for compatibility with older RNAalifold
versions.
- RNAplfold -u now computes all accessibilities up to a maximum length
(much faster than computing each individually)
- ATTENTION: output formats of RNAplfold -u and or RNAup have been changed
Programs parsing RNAplfold and RNAup output will have to be modified.
- RNAfold and RNAalifold compute centroid structures when run with -p
use the -MEA option to compute Maximum Expected Accuracy structures.

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- RNAplfold can now be used to compute accessibilities, i.e. the
probability that a stretch of the RNA remains unpaired (and thus
available for intermolecular interactions).
- A new version of RNAup predicts RNA-RNA interactions takeing into account
the competition between inter- and intramolecular structure in both
molcules
- Circular RNAs can be treated by RNAfold, RNAalifold, RNAsubopt, and RNAcofold
- RNAaliduplex predicts RNA-RNA interactions between two sets of aligned
sequences (inter-molecular structure only)