See Changelog for details. Version 2.0 ------------ - yeeeehaa, its almost done... - 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 - 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.