NEWS

See Changelog for details.

Version 1.8
------------
- 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.

Version 1.7
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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)

Version 1.6
------------
- 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 <mhoechsm@techfak.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

Version 1.5pre 
-----------
- 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

Version 1.4
-----------
- 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().

Version 1.3.1
-------------
- 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).

Version 1.3
-----------
- 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.

Version 1.2.1
-------------
- 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.

Version 1.2
-----------
- New energy parameters from (Walter et.al 1994). 
- Energy parameters can be read from file.
- RNAeval and energy_of_struct() support logarithmic energy function for 
  multi-loops.
- gmlRNA() produces secondary structure drawing in gml (Graph Meta Language). 
- Many bug fixes.