2011-03-10 Ronny Lorenz * 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 * first full pre-release of version 2.0 2009-11-03 Ivo Hofacker * Fix memory corruption in PS_color_aln() 2009-09-09 Ivo Hofacker * 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 * Fix occasional segfault in RNAalifold's print_aliout() 2009-02-24 Ivo Hofacker * Add -MEA options to RNAfold and RNAalifold * change energy_of_alistruct to return float not void 2009-02-24 Ivo Hofacker * 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 * 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 * Add Ribosum matrices for covariance scoring in RNAalifold 2008-06-27 Ivo Hofacker * Change RNAalifold to used berni's new energy evaluation w/o gaps * Add stochastic backtracking in RNAalifold 2008-07-04 Ivo Hofacker * modify output of RNAup (again). Program reading RNAup output will have to updated! 2008-07-02 Ivo Hofacker * 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 * add cofolding to RNAsubopt 2008-01-08 Ivo Hofacker * ensure circfold works even for open chain 2007-12-13 Ulli Mueckstein * upate RNAup related files RNAup can now include the intramolecular structure of both molecules and handles constraints. 2007-12-05 Ronny Lorenz * add circfold variants in part_func.c alipfold.c subopt.c 2007-09-19 Ivo Hofacker * 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 * fix a bug in Lfold() where base number n-max-4 would never pair 2007-08-26 Ivo Hofacker * add RNAaliduplex the alignment version of RNAduplex * introduce a minimal distance between hits produced by duplex_subopt() 2007-07-03 Ivo Hofacker * add a loop_energy() function to compute energy of a single loop 2007-06-23 Ivo Hofacker * add aliLfold() and RNALalifold, alignment variant of Lfold() 2007-04-30 Ivo Hofacker * add RNAup to distribution 2007-04-15 Ivo Hofacker * fix segfault in colorps output (thanks to Andres Varon) 2007-03-03 Ivo Hofacker * avoid unnormalized doubles in scale[], big speedup for pf_fold() on very long sequences 2007-02-03 Ivo Hofacker * RNAalifold can now produce colored structure plots and alignment plots 2007-02-01 Ivo Hofacker * Fix segfault in RNAplfold because of missing prototype 2006-12-01 Ivo Hofacker * RNAduplex would segfault when no structure base pairs are possible 2006-08-22 Ivo Hofacker * add computation stacking probabilities using RNAfold -p2 * add -noPS option for NRAfold to supress drawing structures 2006-08-09 Stephan Bernhart * RNAplfold can now compute probabilites of unpaired regions (scanning version of RNAup) 2006-06-14 Ivo Hofacker * 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 * 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 * fix performance bug in co_pf_fold() * use relative error for termination of Newton iteration 2006-03-02 Ivo Hofacker * add circular folding in alifold() 2006-01-18 Ivo Hofacker * cleanup berni partition cofold code, including several bug fixes 2006-01-16 Ivo Hofacker * update RNAplfold to working version * add PS_dot_plot_turn() in PS_dot.c 2005-11-07 Ivo Hofacker * add new utilities colorna and coloraln 2005-10-11 Christoph Flamm * adapt PS_rna_plot() for drawing co-folded structures 2005-07-24 Ivo Hofacker * fix a few memory problems in structure comparison routines 2005-04-30 Ivo Hofacker * add folding of circular RNAs 2005-03-11 Ivo Hofacker * add -mis option to RNAalifold to give "most informative sequence" as consensus 2005-02-10 Ivo Hofacker * move alifold() into the library 2004-12-22 Stephan Bernhart * add partition function version of RNAcofold 2004-12-23 Ivo Hofacker * add RNApaln for fast structural alignments (RNApdist improvement) 2004-08-12 Ivo Hofacker * fix constrained folding in stochastic backtracking 2004-07-21 Ivo Hofacker * add RNAduplex, to compute hybrid structures without intra-molecular pairs 2004-02-09 Ivo Hofacker * fix bug in fold that caused segfaults when using Intel compiler * add computation of ensemble diversity to RNAfold 2003-09-10 Ivo Hofacker * add annotation options to RNAplot 2003-08-04 Ivo Hofacker * stochastic backtracking finally works. Try e.g. RNAsubopt -p 10 2003-07-18 Ivo Hofacker * add relplot.pl and rotate_ss.pl utilities for reliability annotation and rotation of rna structure plots 2003-01-29 Ivo Hofacker * add RNALfold program to compute locally optimal structures with maximum pair span. * add RNAcofold for computing hybrid structure 2002-11-07 Ivo Hofacker * 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 * 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 * added svg structure plots in PS_dot.c and RNAplot 2002-08-15 Ivo Hofacker * Improve reading of clustal files (alifold) * add a sample alifold.cgi script 2001-09-18 Ivo Hofacker * moved suboptimal folding into the library, thus it's now accessible from the Perl module 2001-08-31 Ivo Hofacker * added co-folding support in energy_of_struct(), and thus RNAeval 2001-04-30 Ivo Hofacker * switch from handcrafted makefiles to automake and autoconf 2001-04-05 Ivo Hofacker * added PS_rna_plot_a to produce structure plots with annotation 2001-03-03 Ivo Hofacker * add alifold; predict consensus structures from alignment 2000-09-28 Ivo Hofacker * add -d3 option to RNAfold for co-axial stacking