1 2011-03-10 Ronny Lorenz <ronny@tbi.univie.ac.at>
2 * new naming scheme for all shipped energy parameter files
3 * fixed bugs that appear while compiling with gcc under MacOS X
4 * fixed bug in RNAup --interaction-first where the longer of the first two
5 sequences was taken as target
6 * added full FASTA input support to RNAfold, RNAcofold, RNAheat, RNAplfold
7 RNALfoldz, RNAsubopt and RNALfold
9 2010-11-24 Ronny Lorenz <ronny@tbi.univie.ac.at>
10 * first full pre-release of version 2.0
12 2009-11-03 Ivo Hofacker <ivo@tbi.univie.ac.at>
13 * Fix memory corruption in PS_color_aln()
15 2009-09-09 Ivo Hofacker <ivo@tbi.univie.ac.at>
16 * Fix bug in RNAplfold when -u and -L parameters are equal
17 * Fix double call to free_arrays() in RNAfold.c
18 * Improve drawing of cofolded structures
21 2009-05-14 Ivo Hofacker <ivo@tbi.univie.ac.at>
23 * Fix occasional segfault in RNAalifold's print_aliout()
26 2009-02-24 Ivo Hofacker <ivo@tbi.univie.ac.at>
28 * Add -MEA options to RNAfold and RNAalifold
29 * change energy_of_alistruct to return float not void
31 2009-02-24 Ivo Hofacker <ivo@tbi.univie.ac.at>
33 * RNAfold will draw structures unless -noPS is used (no more
34 "structure too long" messages)
35 * Restore the "alifold.out" output from RNAalifold -p
36 * RNAalifold -circ did not work due to wrong return type
37 * Accessibility calculation with RNAplfold would give wrong
40 2008-12-03 Ivo Hofacker <ivo@tbi.univie.ac.at>
42 * Add zuker style suboptimals to RNAsubopt (-z)
43 * get_line() should be much faster when reading huge sequences
44 (e.g. whole chromosomes for RNALfold)
46 2008-08-12 Ivo Hofacker <ivo@tbi.univie.ac.at>
48 * Add Ribosum matrices for covariance scoring in RNAalifold
50 2008-06-27 Ivo Hofacker <ivo@tbi.univie.ac.at>
52 * Change RNAalifold to used berni's new energy evaluation w/o gaps
53 * Add stochastic backtracking in RNAalifold
55 2008-07-04 Ivo Hofacker <ivo@tbi.univie.ac.at>
57 * modify output of RNAup (again).
58 Program reading RNAup output will have to updated!
60 2008-07-02 Ivo Hofacker <ivo@tbi.univie.ac.at>
62 * RNAplfold now computes accessibilities for all regions up to a
63 max length simultaneously. Slightly slower when only 1 value is
64 needed, but much faster if all of them are wanted.
65 This entails a new output format. Programs reading accessibility
66 output from RNAplfold need to be updated!
68 2008-03-31 Stephan Bernhart <berni@tbi.univie.ac.at>
70 * add cofolding to RNAsubopt
72 2008-01-08 Ivo Hofacker <ivo@tbi.univie.ac.at>
74 * ensure circfold works even for open chain
76 2007-12-13 Ulli Mueckstein <ulli@tbi.univie.ac.at>
78 * upate RNAup related files
79 RNAup can now include the intramolecular structure of both
80 molecules and handles constraints.
82 2007-12-05 Ronny Lorenz <ronny@tbi.univie.ac.at>
84 * add circfold variants in part_func.c alipfold.c subopt.c
86 2007-09-19 Ivo Hofacker <ivo@tbi.univie.ac.at>
88 * compute the controid structure of the ensemble in RNAfold -p
89 * fix a missing factor 2 in mean_bp_dist().
90 CAUTION ensemble diversities returned by RNAfold -p are now
91 twice as large as in earlier versions.
93 2007-09-04 Ivo Hofacker <ivo@blini.tbi.univie.ac.at>
95 * fix a bug in Lfold() where base number n-max-4 would never pair
97 2007-08-26 Ivo Hofacker <ivo@tbi.univie.ac.at>
99 * add RNAaliduplex the alignment version of RNAduplex
100 * introduce a minimal distance between hits produced by duplex_subopt()
102 2007-07-03 Ivo Hofacker <ivo@tbi.univie.ac.at>
104 * add a loop_energy() function to compute energy of a single loop
106 2007-06-23 Ivo Hofacker <ivo@tbi.univie.ac.at>
108 * add aliLfold() and RNALalifold, alignment variant of Lfold()
110 2007-04-30 Ivo Hofacker <ivo@tbi.univie.ac.at>
111 * add RNAup to distribution
113 2007-04-15 Ivo Hofacker <ivo@tbi.univie.ac.at>
114 * fix segfault in colorps output (thanks to Andres Varon)
116 2007-03-03 Ivo Hofacker <ivo@tbi.univie.ac.at>
117 * avoid unnormalized doubles in scale[], big speedup for pf_fold()
118 on very long sequences
120 2007-02-03 Ivo Hofacker <ivo@tbi.univie.ac.at>
122 * RNAalifold can now produce colored structure plots and
125 2007-02-01 Ivo Hofacker <ivo@tbi.univie.ac.at>
127 * Fix segfault in RNAplfold because of missing prototype
129 2006-12-01 Ivo Hofacker <ivo@tbi.univie.ac.at>
131 * RNAduplex would segfault when no structure base pairs are possible
133 2006-08-22 Ivo Hofacker <ivo@tbi.univie.ac.at>
135 * add computation stacking probabilities using RNAfold -p2
136 * add -noPS option for NRAfold to supress drawing structures
138 2006-08-09 Stephan Bernhart <berni@tbi.univie.ac.at>
140 * RNAplfold can now compute probabilites of unpaired regions
141 (scanning version of RNAup)
143 2006-06-14 Ivo Hofacker <ivo@tbi.univie.ac.at>
145 * compile library with -fpic (if available) for use as shared
146 library in the Perl module.
147 * fix another bug when calling Lfold() repeatedly
148 * fix switch cmdline parsing in RNAalifold (-mis implied -4)
149 * fix bug in cofold() with dangles=0
151 2006-05-08 Ivo Hofacker <ivo@tbi.univie.ac.at>
153 * fix segfault in Lfold() when calling repeatedly
154 * fix structure parsing in RNAstruct.c
155 (thanks to Michael Pheasant for reporting both bugs)
156 * add duplexfold() and alifold() to Perl module
157 * distinguish window size and max pair span in LPfold
159 2006-04-05 Ivo Hofacker <ivo@tbi.univie.ac.at>
161 * fix performance bug in co_pf_fold()
162 * use relative error for termination of Newton iteration
164 2006-03-02 Ivo Hofacker <ivo@tbi.univie.ac.at>
166 * add circular folding in alifold()
168 2006-01-18 Ivo Hofacker <ivo@tbi.univie.ac.at>
170 * cleanup berni partition cofold code, including several bug fixes
172 2006-01-16 Ivo Hofacker <ivo@tbi.univie.ac.at>
174 * update RNAplfold to working version
175 * add PS_dot_plot_turn() in PS_dot.c
177 2005-11-07 Ivo Hofacker <ivo@tbi.univie.ac.at>
179 * add new utilities colorna and coloraln
181 2005-10-11 Christoph Flamm <xtof@tbi.univie.ac.at>
183 * adapt PS_rna_plot() for drawing co-folded structures
185 2005-07-24 Ivo Hofacker <ivo@tbi.univie.ac.at>
187 * fix a few memory problems in structure comparison routines
189 2005-04-30 Ivo Hofacker <ivo@blini.tbi.univie.ac.at>
191 * add folding of circular RNAs
193 2005-03-11 Ivo Hofacker <ivo@blini.tbi.univie.ac.at>
195 * add -mis option to RNAalifold to give "most informative
196 sequence" as consensus
198 2005-02-10 Ivo Hofacker <ivo@tbi.univie.ac.at>
200 * move alifold() into the library
202 2004-12-22 Stephan Bernhart <berni@tbi.univie.ac.at>
204 * add partition function version of RNAcofold
206 2004-12-23 Ivo Hofacker <ivo@tbi.univie.ac.at>
208 * add RNApaln for fast structural alignments (RNApdist improvement)
210 2004-08-12 Ivo Hofacker <ivo@tbi.univie.ac.at>
212 * fix constrained folding in stochastic backtracking
214 2004-07-21 Ivo Hofacker <ivo@tbi.univie.ac.at>
216 * add RNAduplex, to compute hybrid structures without
217 intra-molecular pairs
219 2004-02-09 Ivo Hofacker <ivo@tbi.univie.ac.at>
221 * fix bug in fold that caused segfaults when using Intel compiler
222 * add computation of ensemble diversity to RNAfold
224 2003-09-10 Ivo Hofacker <ivo@tbi.univie.ac.at>
226 * add annotation options to RNAplot
228 2003-08-04 Ivo Hofacker <ivo@tbi.univie.ac.at>
230 * stochastic backtracking finally works. Try e.g.
233 2003-07-18 Ivo Hofacker <ivo@tbi.univie.ac.at>
235 * add relplot.pl and rotate_ss.pl utilities for reliability
236 annotation and rotation of rna structure plots
238 2003-01-29 Ivo Hofacker <ivo@tbi.univie.ac.at>
240 * add RNALfold program to compute locally optimal structures with
242 * add RNAcofold for computing hybrid structure
244 2002-11-07 Ivo Hofacker <ivo@tbi.univie.ac.at>
246 * change Make_bp_profile() and profile_edit_distance() to use
247 simple (float *) arrays; makes Perl access much easier.
248 RNApdist -B now works again
250 2002-10-28 Ivo Hofacker <ivo@tbi.univie.ac.at>
252 * Improved Perl module with pod documentation; allow to write
254 ($structure, $energy) = RNA::fold($seq);
255 Compatibility warning: the ptrvalue() and related functions are
256 gone, see the pod documentation for alternatives.
258 2002-10-29 Ivo Hofacker <ivo@tbi.univie.ac.at>
260 * added svg structure plots in PS_dot.c and RNAplot
262 2002-08-15 Ivo Hofacker <ivo@tbi.univie.ac.at>
264 * Improve reading of clustal files (alifold)
265 * add a sample alifold.cgi script
267 2001-09-18 Ivo Hofacker <ivo@tbi.univie.ac.at>
269 * moved suboptimal folding into the library, thus it's now
270 accessible from the Perl module
272 2001-08-31 Ivo Hofacker <ivo@tbi.univie.ac.at>
274 * added co-folding support in energy_of_struct(), and thus RNAeval
276 2001-04-30 Ivo Hofacker <ivo@tbi.univie.ac.at>
278 * switch from handcrafted makefiles to automake and autoconf
280 2001-04-05 Ivo Hofacker <ivo@tbi.univie.ac.at>
282 * added PS_rna_plot_a to produce structure plots with annotation
284 2001-03-03 Ivo Hofacker <ivo@tbi.univie.ac.at>
286 * add alifold; predict consensus structures from alignment
288 2000-09-28 Ivo Hofacker <ivo@tbi.univie.ac.at>
290 * add -d3 option to RNAfold for co-axial stacking