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ChangeLog
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ChangeLog
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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