--- /dev/null
+See Changelog for details.
+
+Version 2.0
+------------
+- 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
+
+
+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.
+- RNAfold and RNAalifold compute centroid structures when run with -p
+ use the -MEA option to compute Maximum Expected Accuracy structures.
+
+Version 1.7
+------------
+- 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.
git://source.jalview.org / jabaws.git / blobdiff