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
