Viennarna

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- The RNAforester program for tree-alignments of RNA structures is now
distributed with the Vienna RNA package, see the RNAforester
subdirectory for more information. RNAforester was written by Matthias
Hoechsmann <mhoechsmtechfak.uni-bielefeld.de>
- The Kinfold program for stochastic simulation of folding trajectories is
now included in the package, see the Kinfold subdirectory.
- cofolding of two structures now supports suboptimal folding and
partition function folding.
ATTENTION: Energies of hybrid structures now include the Duplex-initiation
energy, which was neglected in previous version.
- RNAplfold is a partition function variant of RNALfold. It computes the
mean probability of a (local) base pair averaged over all sequence
windows that contain the pair.
- new utilities to color alignments and consensus structures
- RNAfold -p now computes the centroid structure
- ATTENTION: ensemble diversities in version <1.6.5 are off by a factor 2

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- ViennaRNA now uses autoconfig generated configure scripts for even better
portability (should compile on any UNIX, Linux, MacOS X, Windows with
Cygwin).
- The new RNAalifold program predicts consensus structures for a set of
aligned sequences.
- Complete suboptimal folding is now integrated in the library.
- Beginning support for co-folding of two strands: energy_of_struct() and
RNAeval can now compute energies of duplex structures.
- RNAcofold predicts hybrid structures of two RNA strands
- RNAduplex predicts hybrid structures, while allowing only inter-molecular
base pairs (useful for finding potential binding sites)
- RNALfold predicts locally stable structures in long sequences.
- Major changes to Perl module. See the pod documentation (perldoc RNA).
- RNAsubopt can do stochastic backtracking to produce samples of suboptimal
structures with Boltzmann statistics.
- New utilities to rotate secondary structure plots and annotate them with
reliability data.
- Various small bug fixes

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- New Turner parameters as described in Mathews et.al. JMB v288, 1999.
Small changes to format of parameter files (old param files won't work!)
- mfe and suboptimal folding will produce only structures without isolated
pairs if noLonelyPairs=1 (-noLP option), for partition function folding
pairs that can only occur as isolated pairs are not formed.
- setting dangles=3 (-d3 option) will allow co-axial stacking of adjacent
helices in mfe folding and energy_of_struct().

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- RNAheat would produce spikes in the specific heat because dangling end
energies did not go smoothly to 0.
- PS dot plots now have an option to use a log scale (edit _dp.ps file
and set logscale to true).

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- Secondary structure plots now use E. Bruccoleri's naview routines for
layout by default. New utility RNAplot produces secondary structure plots
from structures in bracket notation with several options.
- New -d2 option in RNAfold and RNAeval sets dangles=2, which makes
energy_of_struct() and fold() treat dangling ends as in pf_fold().
-noLP option in RNAfold etc sets noLonelyPairs=1, which avoids most
structures containing lonely base pairs (helices of length 1).
- new utility functions pack_structure() unpack_structure() make_pair_table()
and bp_distance(). RNAdistance adds bp_distance() via -DP switch.
- First release of RNAsubopt for complete suboptimal folding.
- fixed bug in asymmetry penalty for interior loops.
- Default compilation now uses doubles for partition function folding.

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- Fixed bug in version 1.2 of the RNAheat program causing overflow errors
for most input sequences.
- The PS_dot_plot() and PS_rna_plot() routines now return an int. The return
value is 0 if the file could not be written, 1 otherwise.
- This version contains the alpha version of a perl5 module, which let's you
access all the capabilities of the Vienna RNA library from perl scripts.