| c0cd936 | Kimmo Palin | 07 November 2012, 13:23:26 UTC | Fixed a variable format clash which sometimes caused core dumps. | 27 January 2015, 14:11:36 UTC |
| f70f2f2 | Kimmo Palin | 07 November 2012, 13:21:41 UTC | Fixed a name clash in alignment format function which trashed showalign with DNA sequences. | 27 January 2015, 14:11:36 UTC |
| 6951c91 | Kimmo Palin | 06 November 2012, 11:25:46 UTC | Improve human readable output | 27 January 2015, 14:11:36 UTC |
| 33a506f | Kimmo Palin | 26 May 2014, 07:43:06 UTC | Revealed computeKLdistaces command and cleared README | 26 May 2014, 07:43:06 UTC |
| 3cfb770 | Kimmo Palin | 02 July 2013, 12:09:36 UTC | Fixed very old and somewhat serious (with negative cutoffs) bug in Motif matching code | 02 July 2013, 12:09:36 UTC |
| 3137a38 | Kimmo Palin | 15 January 2013, 13:36:11 UTC | Made ready for debian packaging | 15 January 2013, 13:36:11 UTC |
| b711d89 | Kimmo Palin | 03 September 2012, 11:24:54 UTC | Fixed documentation for getTFBS | 03 September 2012, 11:24:54 UTC |
| 821cdde | Kimmo Palin | 20 January 2012, 17:03:05 UTC | Renamed a variable for code to work in newer pythons (e.g. 2.7) | 20 January 2012, 17:03:05 UTC |
| 2b5c7c3 | Kimmo Palin | 20 January 2012, 17:02:03 UTC | Removed a trace of CVS legacy | 20 January 2012, 17:02:03 UTC |
| f5b9885 | Kimmo Palin | 20 January 2012, 16:44:06 UTC | User friendliness update | 20 January 2012, 16:44:06 UTC |
| d392ad9 | sksipila | 13 September 2010, 09:34:00 UTC | Finally added the example for the heuristic multiple alignment algorithm. | 13 September 2010, 09:34:00 UTC |
| bc032a4 | sksipila | 14 May 2010, 11:57:09 UTC | Removed some debugging prints | 14 May 2010, 11:57:09 UTC |
| 6d5ce88 | sksipila | 14 May 2010, 11:28:33 UTC | Added a missing } | 14 May 2010, 11:28:33 UTC |
| edabad0 | sksipila | 14 May 2010, 11:26:49 UTC | Defined == in id_triple and added a constructor for Inputs for treeMultipleAlign | 14 May 2010, 11:26:49 UTC |
| a53490b | sksipila | 14 May 2010, 11:11:25 UTC | Added shortMultipleAlign, multiFromPairwise and treeMultipleAlign | 14 May 2010, 11:11:25 UTC |
| a0a95ca | sksipila | 14 May 2010, 10:58:42 UTC | Defined == in id_triple for treeMultiAlign | 14 May 2010, 10:58:42 UTC |
| 3c117fb | sksipila | 14 May 2010, 10:56:23 UTC | *** empty log message *** | 14 May 2010, 10:56:23 UTC |
| 4d5e644 | jazkorho | 25 June 2008, 11:42:57 UTC | Using smaller SCANNING_WINDOW_SIZE by default to limit memory usage. | 25 June 2008, 11:42:57 UTC |
| f24f20e | jazkorho | 24 June 2008, 14:11:01 UTC | Added linebreak to the end. | 24 June 2008, 14:11:01 UTC |
| b8af945 | jazkorho | 24 June 2008, 14:10:05 UTC | Bugfixes. | 24 June 2008, 14:10:05 UTC |
| a467102 | jazkorho | 06 June 2008, 10:56:35 UTC | Finalized new TFBS searching code. Zero-order background version now uses an Aho-Corasick based filter, but the original implementation is still used with Markov background. | 06 June 2008, 10:56:35 UTC |
| 27d27ba | jazkorho | 23 May 2008, 12:10:10 UTC | Switched to a simpler TFBS scanning algorithm due to problems in tests on Murska cluster | 23 May 2008, 12:10:10 UTC |
| 129df35 | jazkorho | 21 May 2008, 11:49:08 UTC | Added comments. | 21 May 2008, 11:49:08 UTC |
| a7e8ed9 | jazkorho | 19 May 2008, 08:19:04 UTC | Added new preprocessor constant for _c_matrix.cc due to new TFBS scanning code. | 19 May 2008, 08:19:04 UTC |
| fd10d39 | jazkorho | 19 May 2008, 08:18:00 UTC | Changed to use the new TFBS search code. | 19 May 2008, 08:18:00 UTC |
| 3e8e05e | jazkorho | 19 May 2008, 08:14:40 UTC | Rewrote TFBS search code. | 19 May 2008, 08:14:40 UTC |
| bd66ec2 | jazkorho | 19 May 2008, 08:14:24 UTC | Rewrote TFBS search code. Scanning with zero-order bg is much faster now. | 19 May 2008, 08:14:24 UTC |
| 6fdf8da | kpalin | 01 April 2008, 05:47:20 UTC | Fixed an indentation. | 01 April 2008, 05:47:20 UTC |
| ce4bb1b | kpalin | 12 March 2008, 12:03:03 UTC | Fixed "documentation" | 12 March 2008, 12:03:03 UTC |
| dcc9ec1 | kpalin | 10 March 2008, 12:55:03 UTC | Added "date-version". | 10 March 2008, 12:55:03 UTC |
| 4bafa00 | kpalin | 29 February 2008, 10:08:23 UTC | Cut motif name from the end. | 29 February 2008, 10:08:23 UTC |
| e8ef1c4 | kpalin | 29 February 2008, 09:10:09 UTC | Report all snps | 29 February 2008, 09:10:09 UTC |
| 1f279d8 | kpalin | 29 February 2008, 08:53:32 UTC | Should provide output even when the memory save was used | 29 February 2008, 08:53:32 UTC |
| 29364cf | kpalin | 02 January 2008, 08:27:14 UTC | Added sequence names and descriptions to GFF output file. | 02 January 2008, 08:27:14 UTC |
| c555cf0 | kpalin | 13 December 2007, 09:39:11 UTC | Pass the c++ memory errors to python exceptions. | 13 December 2007, 09:39:11 UTC |
| 3c1ecb0 | kpalin | 13 December 2007, 09:33:31 UTC | Fixed PFM file name pretty printing and increased temporary GFF file creation limit. | 13 December 2007, 09:33:31 UTC |
| f1a1453 | kpalin | 10 September 2007, 14:19:39 UTC | Korjattiin KL etńisyyksien laskentaa | 10 September 2007, 14:19:39 UTC |
| 9a6d90e | kpalin | 10 September 2007, 14:19:21 UTC | Korjattiin ja nopeutettiin KL-etńisyyksien laskentaa | 10 September 2007, 14:19:21 UTC |
| 8432e10 | kpalin | 09 August 2007, 05:59:59 UTC | Fixed setBGFreq to handle missing sample sequence request gracefully. | 09 August 2007, 05:59:59 UTC |
| f81b142 | kpalin | 09 August 2007, 05:58:02 UTC | Fixed setBGFreq to use sample sequence | 09 August 2007, 05:58:02 UTC |
| bfe3ea2 | kpalin | 09 August 2007, 05:57:36 UTC | Fixed setBGfreq to accept only 1 parameter | 09 August 2007, 05:57:36 UTC |
| 07540b3 | kpalin | 05 June 2007, 12:40:07 UTC | Dont' remember | 05 June 2007, 12:40:07 UTC |
| 7021edb | kpalin | 05 June 2007, 12:39:43 UTC | Just random changes for testing | 05 June 2007, 12:39:43 UTC |
| dea39c9 | kpalin | 24 April 2007, 11:01:06 UTC | Bug hunting without bugs. Added debug printf macro dprintf() | 24 April 2007, 11:01:06 UTC |
| c9ab1ee | kpalin | 14 March 2007, 08:35:58 UTC | Added universal newline support for reading PFM:s | 14 March 2007, 08:35:58 UTC |
| 356bb9f | kpalin | 08 February 2007, 09:22:54 UTC | p-value thresholding now giving impossibly high threshold for motifs with too likely highest scoring match. | 08 February 2007, 09:22:54 UTC |
| 7bf2525 | kpalin | 08 February 2007, 09:21:34 UTC | Added possibility of setting simple background from example. | 08 February 2007, 09:21:34 UTC |
| b2065bd | kpalin | 08 December 2006, 09:51:34 UTC | Added E-values and TFBS p-values | 08 December 2006, 09:51:34 UTC |
| 9ae5fc1 | kpalin | 08 December 2006, 09:49:56 UTC | Fixed a seqfault and added a source file from Pasi rastas which got included in _c_matrix.cc | 08 December 2006, 09:49:56 UTC |
| 876f57e | kpalin | 07 December 2006, 16:21:38 UTC | Added place holders for evalues and fixed a seqfault. | 07 December 2006, 16:21:38 UTC |
| 8ab4c2a | kpalin | 13 November 2006, 13:04:05 UTC | New minor release to Jussi with major improvements. | 13 November 2006, 13:04:05 UTC |
| 6ebbdda | kpalin | 13 November 2006, 13:03:39 UTC | Added RMSE | 13 November 2006, 13:03:39 UTC |
| 8ec3c34 | kpalin | 13 November 2006, 13:03:22 UTC | Added E-model RMSE | 13 November 2006, 13:03:22 UTC |
| f035fff | kpalin | 13 November 2006, 13:03:01 UTC | Added module E-score RMSE | 13 November 2006, 13:03:01 UTC |
| 5208ce3 | kpalin | 13 November 2006, 12:40:58 UTC | Added the parameters of the expectation model to the align_AlignmentObject | 13 November 2006, 12:40:58 UTC |
| e3b778b | kpalin | 13 November 2006, 12:39:23 UTC | Minor usability changes. | 13 November 2006, 12:39:23 UTC |
| c6f419b | kpalin | 13 November 2006, 12:38:02 UTC | Added code for p-value threshold computation. The threshold computation part is from Pasi Rastas. | 13 November 2006, 12:38:02 UTC |
| 07bbeec | kpalin | 13 November 2006, 12:37:09 UTC | Added a constant for rounding range. Linear dependency on the speed of the p-value threshold computation. Unknown, probably mostly positive, dependency on the accuracy of the thresholding. | 13 November 2006, 12:37:09 UTC |
| 13568e0 | kpalin | 13 November 2006, 12:35:22 UTC | Added p-value threshold computation. | 13 November 2006, 12:35:22 UTC |
| 1665e9a | kpalin | 13 November 2006, 12:34:48 UTC | Added TFBS search p-value cutoff and Escore computation. | 13 November 2006, 12:34:48 UTC |
| fd865f2 | kpalin | 13 November 2006, 12:34:15 UTC | Added command to search the binding sites with p-value cutoff. | 13 November 2006, 12:34:15 UTC |
| 4e670cc | kpalin | 13 November 2006, 12:33:41 UTC | Added 50mer tags to the GFF output giving the location of the module. The tags start from the beginning and the end of the module. Added Escore reporting. | 13 November 2006, 12:33:41 UTC |
| bf3e1de | kpalin | 26 October 2006, 08:52:37 UTC | Workaround for old python v2.2 | 26 October 2006, 08:52:37 UTC |
| 12d44ae | kpalin | 19 October 2006, 07:57:30 UTC | Fixed a seqfault. | 19 October 2006, 07:57:30 UTC |
| 4c7d5ef | kpalin | 18 October 2006, 07:23:59 UTC | Added suboptimalsDownTo | 18 October 2006, 07:23:59 UTC |
| 4596fb7 | kpalin | 18 October 2006, 07:23:44 UTC | Added suboptimalsDownTO | 18 October 2006, 07:23:44 UTC |
| 724b659 | kpalin | 18 October 2006, 07:23:28 UTC | Test suboptimalsDownTo command | 18 October 2006, 07:23:28 UTC |
| ef3bad6 | kpalin | 18 October 2006, 06:48:13 UTC | Added testing scripts. | 18 October 2006, 06:48:13 UTC |
| 977726f | kpalin | 27 September 2006, 07:34:55 UTC | Read frequency matrices. | 27 September 2006, 07:34:55 UTC |
| 236411c | kpalin | 26 September 2006, 13:10:45 UTC | Added untested and hidden feature to export PFM as frequency matrix for cisevolver tool. | 26 September 2006, 13:10:45 UTC |
| 7c4fc21 | kpalin | 31 August 2006, 11:19:22 UTC | Align pre-given sequences and get TFBS only if needed. | 31 August 2006, 11:19:22 UTC |
| a130dae | kpalin | 31 August 2006, 10:09:47 UTC | Testing help. | 31 August 2006, 10:09:47 UTC |
| 3dde800 | kpalin | 31 August 2006, 10:09:34 UTC | Minimum remembered pairwise alignments and speed improvements for multi align. | 31 August 2006, 10:09:34 UTC |
| bcab0c3 | kpalin | 31 August 2006, 10:08:36 UTC | More Debug output and TF distance calculations. | 31 August 2006, 10:08:36 UTC |
| c2c9f96 | kpalin | 31 August 2006, 10:07:02 UTC | Random things | 31 August 2006, 10:07:02 UTC |
| 6a7efe7 | kpalin | 29 August 2006, 06:08:40 UTC | Speed improvements. | 29 August 2006, 06:08:40 UTC |
| 1869e71 | kpalin | 25 August 2006, 12:18:54 UTC | Caching distances to pointervec limiter. | 25 August 2006, 12:18:54 UTC |
| 41ada29 | kpalin | 25 August 2006, 12:18:31 UTC | Caching distances to the pointervec limiter. | 25 August 2006, 12:18:31 UTC |
| 2b66482 | kpalin | 14 August 2006, 09:57:30 UTC | Added randomization function and cleaned diagnostic outputs. | 14 August 2006, 09:57:30 UTC |
| c225b0f | kpalin | 14 August 2006, 09:48:06 UTC | Added a new __randomize_full command. | 14 August 2006, 09:48:06 UTC |
| baf25db | kpalin | 14 August 2006, 09:47:34 UTC | Added a quotation mark that was missed during the last checkin. Of course. | 14 August 2006, 09:47:34 UTC |
| 4891567 | kpalin | 14 August 2006, 09:46:06 UTC | Added more comments. | 14 August 2006, 09:46:06 UTC |
| 6ff75ff | kpalin | 14 August 2006, 09:45:41 UTC | Lowered output frequency for the alignment. | 14 August 2006, 09:45:41 UTC |
| 1d598cc | kpalin | 10 August 2006, 11:39:17 UTC | Another try on 64bit port. | 10 August 2006, 11:39:17 UTC |
| 02172d7 | kpalin | 10 August 2006, 11:39:16 UTC | Port to 64bit. Changed custom bit32 type to uint32_t. | 10 August 2006, 11:39:16 UTC |
| 89121cc | kpalin | 12 May 2006, 06:51:05 UTC | Close to perfection. | 12 May 2006, 06:51:05 UTC |
| 68fe39f | kpalin | 11 May 2006, 12:45:35 UTC | Fixed a memory leak. | 11 May 2006, 12:45:35 UTC |
| 2decf05 | kpalin | 11 May 2006, 12:45:05 UTC | Works. But leaks a bit of memory in matrixentry. | 11 May 2006, 12:45:05 UTC |
| 598aa92 | kpalin | 04 May 2006, 07:58:53 UTC | Speed improvements. | 04 May 2006, 07:58:53 UTC |
| 33b739d | kpalin | 03 May 2006, 11:00:17 UTC | Merged. Merged a fix with the main devel. branch. | 03 May 2006, 11:00:17 UTC |
| 162507d | kpalin | 03 May 2006, 10:42:54 UTC | Merged. "Downgrade" version from 2.1 to 2.0pre2 | 03 May 2006, 10:42:54 UTC |
| 90e9c9d | kpalin | 03 May 2006, 10:12:57 UTC | Fixed a nasty bug giving false results depending on order of input sequences. | 03 May 2006, 10:12:57 UTC |
| 1d23a2d | kpalin | 03 May 2006, 10:11:22 UTC | Fixed a bug resulting wrong alignments depending on order of the input sequences. | 03 May 2006, 10:11:22 UTC |
| f2def4b | kpalin | 05 April 2006, 08:30:07 UTC | Regular expressions for sequence removal and commands for multiple alignment. | 05 April 2006, 08:30:07 UTC |
| 0a9cb7e | kpalin | 08 February 2006, 07:44:46 UTC | Fixed faulty asserts. | 08 February 2006, 07:44:46 UTC |
| 99c10ed | kpalin | 11 January 2006, 12:40:46 UTC | More portable shebang line. | 11 January 2006, 12:40:46 UTC |
| 9514190 | kpalin | 05 January 2006, 10:33:45 UTC | Fast and working version. | 05 January 2006, 10:33:45 UTC |
| 7f9c619 | kpalin | 05 January 2006, 09:22:09 UTC | Fast and working version. | 05 January 2006, 09:22:09 UTC |
| a9da21f | kpalin | 05 January 2006, 09:21:54 UTC | Fast and working version. Still needs cleanup. | 05 January 2006, 09:21:54 UTC |
| 0fad5b3 | kpalin | 04 January 2006, 12:29:39 UTC | Almost compatible with multiALign.cc:1.18 | 04 January 2006, 12:29:39 UTC |
