--- /dev/null
+2011-03-10 Ronny Lorenz <ronny@tbi.univie.ac.at>
+ * new naming scheme for all shipped energy parameter files
+ * fixed bugs that appear while compiling with gcc under MacOS X
+ * fixed bug in RNAup --interaction-first where the longer of the first two
+ sequences was taken as target
+ * added full FASTA input support to RNAfold, RNAcofold, RNAheat, RNAplfold
+ RNALfoldz, RNAsubopt and RNALfold
+
+2010-11-24 Ronny Lorenz <ronny@tbi.univie.ac.at>
+ * first full pre-release of version 2.0
+
+2009-11-03 Ivo Hofacker <ivo@tbi.univie.ac.at>
+ * Fix memory corruption in PS_color_aln()
+
+2009-09-09 Ivo Hofacker <ivo@tbi.univie.ac.at>
+ * Fix bug in RNAplfold when -u and -L parameters are equal
+ * Fix double call to free_arrays() in RNAfold.c
+ * Improve drawing of cofolded structures
+
+
+2009-05-14 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * Fix occasional segfault in RNAalifold's print_aliout()
+
+
+2009-02-24 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * Add -MEA options to RNAfold and RNAalifold
+ * change energy_of_alistruct to return float not void
+
+2009-02-24 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * RNAfold will draw structures unless -noPS is used (no more
+ "structure too long" messages)
+ * Restore the "alifold.out" output from RNAalifold -p
+ * RNAalifold -circ did not work due to wrong return type
+ * Accessibility calculation with RNAplfold would give wrong
+ results for u<=30
+
+2008-12-03 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * Add zuker style suboptimals to RNAsubopt (-z)
+ * get_line() should be much faster when reading huge sequences
+ (e.g. whole chromosomes for RNALfold)
+
+2008-08-12 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * Add Ribosum matrices for covariance scoring in RNAalifold
+
+2008-06-27 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * Change RNAalifold to used berni's new energy evaluation w/o gaps
+ * Add stochastic backtracking in RNAalifold
+
+2008-07-04 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * modify output of RNAup (again).
+ Program reading RNAup output will have to updated!
+
+2008-07-02 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * RNAplfold now computes accessibilities for all regions up to a
+ max length simultaneously. Slightly slower when only 1 value is
+ needed, but much faster if all of them are wanted.
+ This entails a new output format. Programs reading accessibility
+ output from RNAplfold need to be updated!
+
+2008-03-31 Stephan Bernhart <berni@tbi.univie.ac.at>
+
+ * add cofolding to RNAsubopt
+
+2008-01-08 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * ensure circfold works even for open chain
+
+2007-12-13 Ulli Mueckstein <ulli@tbi.univie.ac.at>
+
+ * upate RNAup related files
+ RNAup can now include the intramolecular structure of both
+ molecules and handles constraints.
+
+2007-12-05 Ronny Lorenz <ronny@tbi.univie.ac.at>
+
+ * add circfold variants in part_func.c alipfold.c subopt.c
+
+2007-09-19 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * compute the controid structure of the ensemble in RNAfold -p
+ * fix a missing factor 2 in mean_bp_dist().
+ CAUTION ensemble diversities returned by RNAfold -p are now
+ twice as large as in earlier versions.
+
+2007-09-04 Ivo Hofacker <ivo@blini.tbi.univie.ac.at>
+
+ * fix a bug in Lfold() where base number n-max-4 would never pair
+
+2007-08-26 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * add RNAaliduplex the alignment version of RNAduplex
+ * introduce a minimal distance between hits produced by duplex_subopt()
+
+2007-07-03 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * add a loop_energy() function to compute energy of a single loop
+
+2007-06-23 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * add aliLfold() and RNALalifold, alignment variant of Lfold()
+
+2007-04-30 Ivo Hofacker <ivo@tbi.univie.ac.at>
+ * add RNAup to distribution
+
+2007-04-15 Ivo Hofacker <ivo@tbi.univie.ac.at>
+ * fix segfault in colorps output (thanks to Andres Varon)
+
+2007-03-03 Ivo Hofacker <ivo@tbi.univie.ac.at>
+ * avoid unnormalized doubles in scale[], big speedup for pf_fold()
+ on very long sequences
+
+2007-02-03 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * RNAalifold can now produce colored structure plots and
+ alignment plots
+
+2007-02-01 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * Fix segfault in RNAplfold because of missing prototype
+
+2006-12-01 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * RNAduplex would segfault when no structure base pairs are possible
+
+2006-08-22 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * add computation stacking probabilities using RNAfold -p2
+ * add -noPS option for NRAfold to supress drawing structures
+
+2006-08-09 Stephan Bernhart <berni@tbi.univie.ac.at>
+
+ * RNAplfold can now compute probabilites of unpaired regions
+ (scanning version of RNAup)
+
+2006-06-14 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * compile library with -fpic (if available) for use as shared
+ library in the Perl module.
+ * fix another bug when calling Lfold() repeatedly
+ * fix switch cmdline parsing in RNAalifold (-mis implied -4)
+ * fix bug in cofold() with dangles=0
+
+2006-05-08 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * fix segfault in Lfold() when calling repeatedly
+ * fix structure parsing in RNAstruct.c
+ (thanks to Michael Pheasant for reporting both bugs)
+ * add duplexfold() and alifold() to Perl module
+ * distinguish window size and max pair span in LPfold
+
+2006-04-05 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * fix performance bug in co_pf_fold()
+ * use relative error for termination of Newton iteration
+
+2006-03-02 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * add circular folding in alifold()
+
+2006-01-18 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * cleanup berni partition cofold code, including several bug fixes
+
+2006-01-16 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * update RNAplfold to working version
+ * add PS_dot_plot_turn() in PS_dot.c
+
+2005-11-07 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * add new utilities colorna and coloraln
+
+2005-10-11 Christoph Flamm <xtof@tbi.univie.ac.at>
+
+ * adapt PS_rna_plot() for drawing co-folded structures
+
+2005-07-24 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * fix a few memory problems in structure comparison routines
+
+2005-04-30 Ivo Hofacker <ivo@blini.tbi.univie.ac.at>
+
+ * add folding of circular RNAs
+
+2005-03-11 Ivo Hofacker <ivo@blini.tbi.univie.ac.at>
+
+ * add -mis option to RNAalifold to give "most informative
+ sequence" as consensus
+
+2005-02-10 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * move alifold() into the library
+
+2004-12-22 Stephan Bernhart <berni@tbi.univie.ac.at>
+
+ * add partition function version of RNAcofold
+
+2004-12-23 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * add RNApaln for fast structural alignments (RNApdist improvement)
+
+2004-08-12 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * fix constrained folding in stochastic backtracking
+
+2004-07-21 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * add RNAduplex, to compute hybrid structures without
+ intra-molecular pairs
+
+2004-02-09 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * fix bug in fold that caused segfaults when using Intel compiler
+ * add computation of ensemble diversity to RNAfold
+
+2003-09-10 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * add annotation options to RNAplot
+
+2003-08-04 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * stochastic backtracking finally works. Try e.g.
+ RNAsubopt -p 10
+
+2003-07-18 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * add relplot.pl and rotate_ss.pl utilities for reliability
+ annotation and rotation of rna structure plots
+
+2003-01-29 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * add RNALfold program to compute locally optimal structures with
+ maximum pair span.
+ * add RNAcofold for computing hybrid structure
+
+2002-11-07 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * change Make_bp_profile() and profile_edit_distance() to use
+ simple (float *) arrays; makes Perl access much easier.
+ RNApdist -B now works again
+
+2002-10-28 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * Improved Perl module with pod documentation; allow to write
+ things like
+ ($structure, $energy) = RNA::fold($seq);
+ Compatibility warning: the ptrvalue() and related functions are
+ gone, see the pod documentation for alternatives.
+
+2002-10-29 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * added svg structure plots in PS_dot.c and RNAplot
+
+2002-08-15 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * Improve reading of clustal files (alifold)
+ * add a sample alifold.cgi script
+
+2001-09-18 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * moved suboptimal folding into the library, thus it's now
+ accessible from the Perl module
+
+2001-08-31 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * added co-folding support in energy_of_struct(), and thus RNAeval
+
+2001-04-30 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * switch from handcrafted makefiles to automake and autoconf
+
+2001-04-05 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * added PS_rna_plot_a to produce structure plots with annotation
+
+2001-03-03 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * add alifold; predict consensus structures from alignment
+
+2000-09-28 Ivo Hofacker <ivo@tbi.univie.ac.at>
+
+ * add -d3 option to RNAfold for co-axial stacking
git://source.jalview.org / jabaws.git / blobdiff