1 See Changelog for details.
5 - Meanwhile, a lot of changes in the RNAlib have accumulated. See the Reference
6 Manual and the Changelog for further details
7 - All algorithms use the Turner'04 nearest neighbor model
8 - The RNAlib provides (OpenMP) threadsafe folding routines per default. This is
9 enables concurrent calls to the folding routines in parallel. The feature
10 can be disabled by passing '--disable-openmp' to the configure script
11 - serious changes in command line parameters. Everything complies with
12 GNU standard from now on (short options with preceding '-', long options
14 - FASTA file support for RNAfold. RNA sequences do not need to be passed
15 on a single line anymore when a FASTA header is provided.
16 - The new program RNA2Dfold computes MFE, partition function and
17 stochastically sampled secondary structures in a partitioning of the secondary
18 structure space according to the base pair distance to two reference structures
19 - The new program PKplex computes...
20 - The new program RNALfoldz computes locally stable secondary structures
21 together with a z-score
22 - The new program RNALalifold computes locally stable consensus structures for
24 - The new program RNAparconv enables the conversion of 'old' energy parameter files
25 (v1.4-v1.8) to the new format used in version 2.x
30 - new RNAalifold has better treatment of gaps and ribosum based covariance
31 scores. Use the -old switch for compatibility with older RNAalifold
33 - RNAplfold -u now computes all accessibilities up to a maximum length
34 (much faster than computing each individually)
35 - ATTENTION: output formats of RNAplfold -u and or RNAup have been changed
36 Programs parsing RNAplfold and RNAup output will have to be modified.
37 - RNAfold and RNAalifold compute centroid structures when run with -p
38 use the -MEA option to compute Maximum Expected Accuracy structures.
42 - RNAplfold can now be used to compute accessibilities, i.e. the
43 probability that a stretch of the RNA remains unpaired (and thus
44 available for intermolecular interactions).
45 - A new version of RNAup predicts RNA-RNA interactions takeing into account
46 the competition between inter- and intramolecular structure in both
48 - Circular RNAs can be treated by RNAfold, RNAalifold, RNAsubopt, and RNAcofold
49 - RNAaliduplex predicts RNA-RNA interactions between two sets of aligned
50 sequences (inter-molecular structure only)
54 - The RNAforester program for tree-alignments of RNA structures is now
55 distributed with the Vienna RNA package, see the RNAforester
56 subdirectory for more information. RNAforester was written by Matthias
57 Hoechsmann <mhoechsm@techfak.uni-bielefeld.de>
58 - The Kinfold program for stochastic simulation of folding trajectories is
59 now included in the package, see the Kinfold subdirectory.
60 - cofolding of two structures now supports suboptimal folding and
61 partition function folding.
62 ATTENTION: Energies of hybrid structures now include the Duplex-initiation
63 energy, which was neglected in previous version.
64 - RNAplfold is a partition function variant of RNALfold. It computes the
65 mean probability of a (local) base pair averaged over all sequence
66 windows that contain the pair.
67 - new utilities to color alignments and consensus structures
68 - RNAfold -p now computes the centroid structure
69 - ATTENTION: ensemble diversities in version <1.6.5 are off by a factor 2
73 - ViennaRNA now uses autoconfig generated configure scripts for even better
74 portability (should compile on any UNIX, Linux, MacOS X, Windows with
76 - The new RNAalifold program predicts consensus structures for a set of
78 - Complete suboptimal folding is now integrated in the library.
79 - Beginning support for co-folding of two strands: energy_of_struct() and
80 RNAeval can now compute energies of duplex structures.
81 - RNAcofold predicts hybrid structures of two RNA strands
82 - RNAduplex predicts hybrid structures, while allowing only inter-molecular
83 base pairs (useful for finding potential binding sites)
84 - RNALfold predicts locally stable structures in long sequences.
85 - Major changes to Perl module. See the pod documentation (perldoc RNA).
86 - RNAsubopt can do stochastic backtracking to produce samples of suboptimal
87 structures with Boltzmann statistics.
88 - New utilities to rotate secondary structure plots and annotate them with
90 - Various small bug fixes
94 - New Turner parameters as described in Mathews et.al. JMB v288, 1999.
95 Small changes to format of parameter files (old param files won't work!)
96 - mfe and suboptimal folding will produce only structures without isolated
97 pairs if noLonelyPairs=1 (-noLP option), for partition function folding
98 pairs that can only occur as isolated pairs are not formed.
99 - setting dangles=3 (-d3 option) will allow co-axial stacking of adjacent
100 helices in mfe folding and energy_of_struct().
104 - RNAheat would produce spikes in the specific heat because dangling end
105 energies did not go smoothly to 0.
106 - PS dot plots now have an option to use a log scale (edit _dp.ps file
107 and set logscale to true).
111 - Secondary structure plots now use E. Bruccoleri's naview routines for
112 layout by default. New utility RNAplot produces secondary structure plots
113 from structures in bracket notation with several options.
114 - New -d2 option in RNAfold and RNAeval sets dangles=2, which makes
115 energy_of_struct() and fold() treat dangling ends as in pf_fold().
116 -noLP option in RNAfold etc sets noLonelyPairs=1, which avoids most
117 structures containing lonely base pairs (helices of length 1).
118 - new utility functions pack_structure() unpack_structure() make_pair_table()
119 and bp_distance(). RNAdistance adds bp_distance() via -DP switch.
120 - First release of RNAsubopt for complete suboptimal folding.
121 - fixed bug in asymmetry penalty for interior loops.
122 - Default compilation now uses doubles for partition function folding.
126 - Fixed bug in version 1.2 of the RNAheat program causing overflow errors
127 for most input sequences.
128 - The PS_dot_plot() and PS_rna_plot() routines now return an int. The return
129 value is 0 if the file could not be written, 1 otherwise.
130 - This version contains the alpha version of a perl5 module, which let's you
131 access all the capabilities of the Vienna RNA library from perl scripts.
135 - New energy parameters from (Walter et.al 1994).
136 - Energy parameters can be read from file.
137 - RNAeval and energy_of_struct() support logarithmic energy function for
139 - gmlRNA() produces secondary structure drawing in gml (Graph Meta Language).