| 8c7bcb9 | Ronny Lorenz | 04 May 2015, 13:34:31 UTC | Merge v2.1.6 | 04 May 2015, 13:34:31 UTC |
| 7c331b1 | Ronny Lorenz | 04 May 2015, 13:34:30 UTC | Merge v2.1.5 | 04 May 2015, 13:34:30 UTC |
| fa00faf | Ronny Lorenz | 04 May 2015, 13:34:29 UTC | Merge v2.1.4 | 04 May 2015, 13:34:29 UTC |
| 8d01df7 | Ronny Lorenz | 04 May 2015, 13:34:29 UTC | Merge v2.1.3 | 04 May 2015, 13:34:29 UTC |
| 93e49c7 | Ronny Lorenz | 04 May 2015, 13:34:28 UTC | Merge v2.1.2 | 04 May 2015, 13:34:28 UTC |
| 4bc72a2 | Ronny Lorenz | 04 May 2015, 13:34:27 UTC | Merge v2.1.1 | 04 May 2015, 13:34:27 UTC |
| 06198b6 | Ronny Lorenz | 04 May 2015, 13:34:25 UTC | Merge v2.1.0 | 04 May 2015, 13:34:25 UTC |
| abdbf85 | Ronny Lorenz | 04 May 2015, 13:34:06 UTC | Merge v2.0.7 | 04 May 2015, 13:34:06 UTC |
| f3e2b22 | Ronny Lorenz | 04 May 2015, 13:34:05 UTC | Merge v2.0.6 | 04 May 2015, 13:34:05 UTC |
| d3262c8 | Ronny Lorenz | 04 May 2015, 13:34:04 UTC | Merge v2.0.5 | 04 May 2015, 13:34:04 UTC |
| 65e147f | Ronny Lorenz | 04 May 2015, 13:34:04 UTC | Merge v2.0.4 | 04 May 2015, 13:34:04 UTC |
| 48c40ba | Ronny Lorenz | 04 May 2015, 13:34:03 UTC | Merge v2.0.3 | 04 May 2015, 13:34:03 UTC |
| bde7173 | Ronny Lorenz | 04 May 2015, 13:34:02 UTC | Merge v2.0.2 | 04 May 2015, 13:34:02 UTC |
| c7cbca5 | Ronny Lorenz | 04 May 2015, 13:34:00 UTC | Merge v2.0.1 | 04 May 2015, 13:34:00 UTC |
| c4d170c | Ronny Lorenz | 04 May 2015, 13:32:41 UTC | Merge v2.0RC4 | 04 May 2015, 13:32:41 UTC |
| c5ddc5a | Ivo Hofacker | 07 March 2012, 18:22:09 UTC | update Kinfold submodule to new HEAD | 07 March 2012, 18:22:09 UTC |
| 6e79871 | Ivo Hofacker | 23 February 2012, 11:12:47 UTC | trivialities | 23 February 2012, 11:12:47 UTC |
| cf46acf | Ivo Hofacker | 09 March 2011, 07:44:16 UTC | Update submodule | 09 March 2011, 07:44:16 UTC |
| dd5e4df | Ivo Hofacker | 28 February 2011, 20:07:28 UTC | bump version, fix whitespace | 28 February 2011, 20:07:28 UTC |
| 4fb4162 | Ivo Hofacker | 04 February 2011, 07:38:57 UTC | Make sure pair_math can be used with c++ compilers | 04 February 2011, 07:38:57 UTC |
| 21178a8 | Ivo Hofacker | 04 February 2011, 07:35:12 UTC | Avoid out of bound memory access when length<5 (reported by Michiel de Hoon) | 04 February 2011, 07:35:12 UTC |
| 559ee1e | Ivo Hofacker | 08 July 2010, 08:26:30 UTC | Can't use -o and -u at the same time, add check and error msg | 08 July 2010, 08:26:30 UTC |
| e5e7e87 | Ivo Hofacker | 18 April 2010, 17:28:50 UTC | Fix a missing TermAU when the very last base pairs. | 18 April 2010, 17:28:50 UTC |
| 6430697 | Ivo Hofacker | 08 April 2010, 07:39:54 UTC | Fix stochastic backtracking in RNAalifold. Bump version. | 08 April 2010, 07:39:54 UTC |
| 528f3fd | Ivo Hofacker | 28 March 2010, 11:11:40 UTC | Update documenation. | 28 March 2010, 11:11:40 UTC |
| 0875314 | Ivo Hofacker | 10 November 2009, 11:20:13 UTC | ensure that cut_point is within sequence before calling cofold() | 10 November 2009, 11:20:13 UTC |
| 5164513 | Ivo Hofacker | 03 November 2009, 18:06:23 UTC | Add Kinfold as submodule | 03 November 2009, 18:06:23 UTC |
| 548c817 | Ivo Hofacker | 03 November 2009, 15:29:09 UTC | Fix out-of-bounds write in PS_color_aln() | 03 November 2009, 15:29:09 UTC |
| 4528ead | Ivo Hofacker | 13 October 2009, 13:06:55 UTC | bump version | 13 October 2009, 13:06:55 UTC |
| 61a47ad | Ivo Hofacker | 13 October 2009, 11:41:14 UTC | Fix the LPfold bug for real | 13 October 2009, 11:41:14 UTC |
| 2d1e853 | Ivo Hofacker | 30 September 2009, 15:14:46 UTC | Fix bug in LPfold when winSize (-L) and ulength (-u) are equal. Also add special case for ulength=winSize | 30 September 2009, 15:14:46 UTC |
| 61e0335 | Ivo Hofacker | 09 September 2009, 06:43:18 UTC | Add missing MEA.h file Fix double call to free_arrays() in RNAfold.c | 09 September 2009, 06:43:18 UTC |
| 474eb9c | Ivo Hofacker | 09 September 2009, 06:38:42 UTC | Improve drawing of cofolded structures | 09 September 2009, 06:38:42 UTC |
| 215f965 | Ivo Hofacker | 29 June 2009, 14:38:57 UTC | Bump to version 1.8.3 | 29 June 2009, 14:38:57 UTC |
| 5b7bb6d | Ivo Hofacker | 29 June 2009, 14:34:34 UTC | Add Lfold() wrapper to RNA.i The ushortP_... array functions access arrays of unsigned signed short, while shortP_... can only be used for short (this might break existing Perl code). | 29 June 2009, 14:34:34 UTC |
| 2234ba0 | Ivo Hofacker | 18 June 2009, 12:40:49 UTC | Rewrite the MEA() code to use the same definition of expected accuracy as in Do et al. (2006) | 18 June 2009, 12:40:49 UTC |
| c30e492 | Ivo Hofacker | 19 May 2009, 14:43:09 UTC | make sure entries in scale[] decrease to 0 (apply fix from part_func.c to part_func_co.c and part_func_up.c) | 19 May 2009, 14:43:09 UTC |
| 1a51784 | Ivo Hofacker | 14 May 2009, 12:02:39 UTC | Make sure the duck[] array is allocated with correct size | 14 May 2009, 12:02:39 UTC |
| 60afb03 | Ivo Hofacker | 12 May 2009, 12:59:01 UTC | Always produce of PS plot unless -noPS is given | 12 May 2009, 12:59:01 UTC |
| 0887172 | bernling | 12 May 2009, 12:27:17 UTC | added test for pf_cofold and concentration computation | 12 May 2009, 12:35:13 UTC |
| f56a65e | bernling | 11 May 2009, 13:34:53 UTC | dded -noPS to RNAcofold.c | 12 May 2009, 12:35:12 UTC |
| ea1253f | bernling | 29 April 2009, 13:56:24 UTC | Added get_concentrations for co_pf_fold, also added documentation | 12 May 2009, 12:35:12 UTC |
| 63f03d4 | bernling | 28 April 2009, 14:50:12 UTC | added perl binding for co_pf_fold in RNA.i and a test in test.pl | 12 May 2009, 12:35:12 UTC |
| 4e08ea3 | Ivo Hofacker | 01 May 2009, 10:52:29 UTC | Bring help messges and man pages in sync with actual options | 01 May 2009, 10:52:29 UTC |
| c68fc22 | Ivo Hofacker | 24 April 2009, 11:17:07 UTC | Add maximum expected accuracy folding in MEA.c Add -MEA options to RNAfold and RNAalifold | 24 April 2009, 11:17:07 UTC |
| c4d546d | Ivo Hofacker | 24 April 2009, 09:42:42 UTC | change energy_of_alistruct to return float not void | 24 April 2009, 09:42:42 UTC |
| 69fe067 | Ivo Hofacker | 19 March 2009, 09:45:28 UTC | cvsimport | 19 March 2009, 09:45:28 UTC |
| 5de9486 | Ivo Hofacker | 20 March 2009, 21:26:36 UTC | automake wants AM_PROG_CC_C_O not AC_... | 20 March 2009, 21:26:36 UTC |
| dbb805c | Ivo Hofacker | 19 March 2009, 09:45:28 UTC | Special case for open chain (gave segfault) | 19 March 2009, 09:45:28 UTC |
| 01551f5 | ivo | 12 March 2009, 15:08:19 UTC | *** empty log message *** | 12 March 2009, 15:08:19 UTC |
| 1dc6cc2 | ivo | 27 February 2009, 16:25:54 UTC | fix typo in last patch | 27 February 2009, 16:25:54 UTC |
| 6f9d918 | ivo | 24 February 2009, 15:56:08 UTC | Fix mismatched return type between alifold.h/alifold.c | 24 February 2009, 15:56:08 UTC |
| 6e747fa | ivo | 24 February 2009, 14:22:21 UTC | Always do PS structure plot, unless -noPS is used | 24 February 2009, 14:22:21 UTC |
| fe0b096 | ivo | 24 February 2009, 14:21:26 UTC | In alignments of two seqs, two columns without any canonical pair could pair. Restore the alifold.out output lost after major alifold update. | 24 February 2009, 14:21:26 UTC |
| dcf6be9 | ivo | 18 February 2009, 20:34:38 UTC | Fixed P_unpaired calculation for u<31 | 18 February 2009, 20:34:38 UTC |
| b1b6194 | ivo | 12 February 2009, 14:10:31 UTC | *** empty log message *** | 12 February 2009, 14:10:31 UTC |
| 9a3b872 | ivo | 13 January 2009, 17:49:58 UTC | Fix typo | 13 January 2009, 17:49:58 UTC |
| b511642 | ivo | 16 December 2008, 22:30:30 UTC | get_line was still wrong | 16 December 2008, 22:30:30 UTC |
| a0749e0 | ivo | 09 December 2008, 17:30:57 UTC | *** empty log message *** | 09 December 2008, 17:30:57 UTC |
| ff1f53f | ivo | 03 December 2008, 16:55:44 UTC | add Zuker style suboptimals. Implemnted by abusing the cofold() code. | 03 December 2008, 16:55:44 UTC |
| 86db769 | ivo | 03 December 2008, 16:54:20 UTC | *** empty log message *** | 03 December 2008, 16:54:20 UTC |
| cc424f6 | ivo | 26 November 2008, 16:10:55 UTC | avoid accessing Ss[s][-1] in case of endgaps | 26 November 2008, 16:10:55 UTC |
| d1f31be | ivo | 26 November 2008, 16:04:14 UTC | fix bug in energy_of_alistruct | 26 November 2008, 16:04:14 UTC |
| d1395d5 | ivo | 25 November 2008, 15:39:23 UTC | fix get_line for real | 25 November 2008, 15:39:23 UTC |
| 22f8942 | ivo | 25 November 2008, 15:02:30 UTC | fix the fixed get_line() | 25 November 2008, 15:02:30 UTC |
| 1dda88f | ivo | 01 November 2008, 21:10:20 UTC | avoid rounding errors when computing DoS | 01 November 2008, 21:10:20 UTC |
| a28421d | ivo | 01 November 2008, 21:04:23 UTC | add man page RNAaliduplex.1 | 01 November 2008, 21:04:23 UTC |
| d99389d | ivo | 01 November 2008, 19:03:07 UTC | Used cofold() without including cofold.h; switched back to fold() for now. | 01 November 2008, 19:03:07 UTC |
| 64dcfed | ivo | 21 October 2008, 09:54:24 UTC | *** empty log message *** | 21 October 2008, 09:54:24 UTC |
| 7b0ad57 | ivo | 20 October 2008, 09:01:46 UTC | Avoid excessive reallocs in get_line (slow when reading whole chromosomes) | 20 October 2008, 09:01:46 UTC |
| 588f142 | ivo | 09 October 2008, 15:42:45 UTC | make sure path_fwd is initialized. | 09 October 2008, 15:42:45 UTC |
| 75f8283 | ivo | 09 October 2008, 07:19:17 UTC | add simple path search tool for refolding barrier between two conformations | 09 October 2008, 07:19:17 UTC |
| 9bf1110 | ivo | 09 October 2008, 07:17:12 UTC | comment out non-existing functions | 09 October 2008, 07:17:12 UTC |
| 91867cc | ivo | 09 October 2008, 07:11:21 UTC | avoid computing log(0) | 09 October 2008, 07:11:21 UTC |
| 7630da9 | ivo | 09 October 2008, 07:07:43 UTC | update | 09 October 2008, 07:07:43 UTC |
| 066f6fd | ivo | 04 September 2008, 11:22:56 UTC | *** empty log message *** | 04 September 2008, 11:22:56 UTC |
| 53b0f50 | ivo | 02 September 2008, 08:59:40 UTC | *** empty log message *** | 02 September 2008, 08:59:40 UTC |
| 26cf168 | ivo | 12 August 2008, 19:49:27 UTC | update | 12 August 2008, 19:49:27 UTC |
| ff34895 | ivo | 12 August 2008, 19:47:29 UTC | add ribo.[ch] Ribosum matrices and selection code | 12 August 2008, 19:47:29 UTC |
| 5bfbc65 | ivo | 12 August 2008, 19:44:20 UTC | update | 12 August 2008, 19:44:20 UTC |
| ba41dd6 | ivo | 12 August 2008, 19:43:34 UTC | Ribosum matrices are compiled in. Best matrix is chosen automatically unless specified | 12 August 2008, 19:43:34 UTC |
| c9bf13c | ivo | 12 August 2008, 09:25:27 UTC | last update accidentally switched of color alingmnet output | 12 August 2008, 09:25:27 UTC |
| b50ddaf | ivo | 04 July 2008, 14:29:14 UTC | pf.expMLbase contained energies instead of Boltzman weights | 04 July 2008, 14:29:14 UTC |
| eaea908 | ivo | 04 July 2008, 14:27:09 UTC | Modify output (again) | 04 July 2008, 14:27:09 UTC |
| 4840026 | ivo | 02 July 2008, 15:54:06 UTC | Sync man pages to last updates | 02 July 2008, 15:54:06 UTC |
| a6560d6 | ivo | 02 July 2008, 15:34:06 UTC | update accessibility calculation in LPfold.c now computes accessibility for regions of all sizes up to a maximum (instead just one) In most cases it's nevertheless faster than the old version | 02 July 2008, 15:34:06 UTC |
| 34508c0 | ivo | 27 June 2008, 16:17:11 UTC | Change alifold to use berni's new energy evaluation w/o gaps Add stochastic backtracking to alipfold Add energy_of_alistruct() | 27 June 2008, 16:17:11 UTC |
| 262dd25 | ivo | 03 June 2008, 22:34:05 UTC | Use $(srcdir)/../H to allow remote configure | 03 June 2008, 22:34:05 UTC |
| 6282f95 | ivo | 03 June 2008, 22:31:05 UTC | *** empty log message *** | 03 June 2008, 22:31:05 UTC |
| 2cc2870 | ivo | 03 June 2008, 22:30:11 UTC | set prefix for installation of Perl module via PERLPREFIX | 03 June 2008, 22:30:11 UTC |
| 11bcd43 | ivo | 03 June 2008, 21:19:42 UTC | reset winsize for each sequence in case winsize<length | 03 June 2008, 21:19:42 UTC |
| 0c5df96 | ivo | 03 June 2008, 15:01:41 UTC | use xrealloc() helper function | 03 June 2008, 15:01:41 UTC |
| b003a02 | ivo | 08 May 2008, 14:13:05 UTC | add encode_seq() helper function | 08 May 2008, 14:13:05 UTC |
| 8c5016d | ivo | 08 May 2008, 14:11:55 UTC | minor output changes | 08 May 2008, 14:11:55 UTC |
| 883ebf8 | ivo | 31 March 2008, 15:06:40 UTC | Add cofolding support in subopt | 31 March 2008, 15:06:40 UTC |
| 5e8b01e | ivo | 27 March 2008, 11:34:31 UTC | clarify use of make_tree and expand_Full | 27 March 2008, 11:34:31 UTC |
| de716db | ivo | 26 March 2008, 14:12:59 UTC | *** empty log message *** | 26 March 2008, 14:12:59 UTC |
| abe5de3 | ivo | 25 March 2008, 15:41:48 UTC | add strdup header (for ansi pedantic compilers) | 25 March 2008, 15:41:48 UTC |
| 3e39ef5 | ivo | 25 March 2008, 14:45:03 UTC | fix p_unpaired for regions at the ends of the sequence | 25 March 2008, 14:45:03 UTC |
| 9f12fc4 | ivo | 06 March 2008, 16:45:56 UTC | *** empty log message *** | 06 March 2008, 16:45:56 UTC |
