| 8231d56 | Mikhail Kolmogorov | 30 May 2015, 02:21:56 UTC | logging + chromosome script | 30 May 2015, 02:21:56 UTC |
| 79b20f7 | Mikhail Kolmogorov | 26 May 2015, 19:05:33 UTC | chromosome fusions script | 26 May 2015, 19:05:33 UTC |
| b214415 | Mikhail Kolmogorov | 26 May 2015, 02:06:52 UTC | debugging improvements | 26 May 2015, 02:06:52 UTC |
| 42a3c5d | Mikhail Kolmogorov | 25 May 2015, 20:34:47 UTC | k-breaks and some fixes in output generation and contig breaks | 25 May 2015, 20:34:47 UTC |
| 893a76f | Mikhail Kolmogorov | 23 May 2015, 20:35:59 UTC | fix in rearrangements projecting | 23 May 2015, 20:35:59 UTC |
| 61e3e3e | Mikhail Kolmogorov | 22 May 2015, 20:17:24 UTC | inferer instead of refiner on the last stage | 22 May 2015, 20:17:24 UTC |
| a3a0dd2 | Mikhail Kolmogorov | 22 May 2015, 04:18:32 UTC | more accurate adjacency refinement | 22 May 2015, 04:18:32 UTC |
| e0d3f3e | Mikhail Kolmogorov | 22 May 2015, 02:52:41 UTC | more accurate low-level scaffold structure | 22 May 2015, 02:52:41 UTC |
| 0627959 | Mikhail Kolmogorov | 21 May 2015, 00:35:25 UTC | debug dir fix | 21 May 2015, 00:35:25 UTC |
| 91bacb8 | Mikhail Kolmogorov | 21 May 2015, 00:30:52 UTC | correct contig links for refiner module | 21 May 2015, 00:30:52 UTC |
| 536a1fd | Mikhail Kolmogorov | 18 May 2015, 00:45:14 UTC | conservative assembly + refinement in the end + partial fix of distance estimation | 18 May 2015, 00:45:14 UTC |
| ed8ec16 | Mikhail Kolmogorov | 17 May 2015, 02:20:12 UTC | small fix in rearrangement projection + Helicobacter test removed | 17 May 2015, 02:20:12 UTC |
| 8011ca8 | Mikhail Kolmogorov | 17 May 2015, 01:55:57 UTC | some adjustments + fixed distances and supporting genomes | 17 May 2015, 01:55:57 UTC |
| 57143f6 | Mikhail Kolmogorov | 16 May 2015, 00:13:58 UTC | back to iterative BG + working rearrangements projection | 16 May 2015, 00:13:58 UTC |
| 681fbff | Mikhail Kolmogorov | 14 May 2015, 00:39:39 UTC | and adhoc implementation of rearrangement projection | 14 May 2015, 00:39:39 UTC |
| c8c62eb | Mikhail Kolmogorov | 13 May 2015, 02:41:16 UTC | iterative contig breaks | 13 May 2015, 02:41:16 UTC |
| b8a8432 | Mikhail Kolmogorov | 12 May 2015, 19:57:14 UTC | handling rare case in chimera detector | 12 May 2015, 19:57:14 UTC |
| 633c4c9 | Mikhail Kolmogorov | 12 May 2015, 01:35:59 UTC | iterative contig breakage | 12 May 2015, 01:35:59 UTC |
| 79c73f5 | Mikhail Kolmogorov | 09 May 2015, 06:11:41 UTC | inversions recognition | 09 May 2015, 06:11:41 UTC |
| 2a212a1 | Mikhail Kolmogorov | 08 May 2015, 20:29:04 UTC | some extra debug features | 08 May 2015, 20:29:04 UTC |
| dc9d0a7 | Mikhail Kolmogorov | 08 May 2015, 03:16:51 UTC | more relaxed chimera detection | 08 May 2015, 03:16:51 UTC |
| 43bd350 | Mikhail Kolmogorov | 07 May 2015, 02:35:44 UTC | minimum gap size | 07 May 2015, 02:35:44 UTC |
| 8a6cc58 | Mikhail Kolmogorov | 06 May 2015, 18:38:02 UTC | fix in alternating cycle search | 06 May 2015, 18:38:02 UTC |
| 5f61ed5 | Mikhail Kolmogorov | 06 May 2015, 04:50:59 UTC | slowness fixed | 06 May 2015, 04:50:59 UTC |
| e56a232 | Mikhail Kolmogorov | 06 May 2015, 00:08:32 UTC | faster chimer detection | 06 May 2015, 00:08:32 UTC |
| 48e26ab | Mikhail Kolmogorov | 05 May 2015, 23:21:22 UTC | some refactoring | 05 May 2015, 23:21:22 UTC |
| 8f07fce | Mikhail Kolmogorov | 05 May 2015, 22:17:54 UTC | draft sequences with rr | 05 May 2015, 22:17:54 UTC |
| a8eaa08 | Mikhail Kolmogorov | 01 May 2015, 21:39:28 UTC | bux with coordinates | 01 May 2015, 21:39:28 UTC |
| fbff3df | Mikhail Kolmogorov | 01 May 2015, 21:27:09 UTC | fasta statistics fix | 01 May 2015, 21:27:09 UTC |
| e02fc42 | Mikhail Kolmogorov | 01 May 2015, 20:46:33 UTC | cutting contigs + tests fix | 01 May 2015, 20:46:33 UTC |
| ccc6c22 | Mikhail Kolmogorov | 01 May 2015, 01:05:35 UTC | fix for debug mode | 01 May 2015, 01:05:35 UTC |
| d048f03 | Mikhail Kolmogorov | 01 May 2015, 00:12:57 UTC | fixed bug with permutation attributes | 01 May 2015, 00:12:57 UTC |
| 6e04d5c | Mikhail Kolmogorov | 30 April 2015, 23:54:26 UTC | new method for chimera detection | 30 April 2015, 23:54:26 UTC |
| 91cee0c | Mikhail Kolmogorov | 30 April 2015, 03:25:44 UTC | final refactoring | 30 April 2015, 03:25:44 UTC |
| 20d1c11 | Mikhail Kolmogorov | 29 April 2015, 22:23:30 UTC | major refactoring | 29 April 2015, 22:23:30 UTC |
| b4d82ec | Mikhail Kolmogorov | 29 April 2015, 02:03:33 UTC | keep only those blocks that represented exactly once at first stage | 29 April 2015, 02:03:33 UTC |
| 97ec218 | Mikhail Kolmogorov | 29 April 2015, 00:11:01 UTC | faster version + rr only on last stage | 29 April 2015, 00:11:01 UTC |
| 0af3bd1 | Mikhail Kolmogorov | 27 April 2015, 22:55:45 UTC | trying to incorporate canddidate adjacencies | 27 April 2015, 22:55:45 UTC |
| d342b92 | Mikhail Kolmogorov | 27 April 2015, 02:21:54 UTC | a fix for permutations from one block | 27 April 2015, 02:21:54 UTC |
| f9e01c6 | Mikhail Kolmogorov | 27 April 2015, 00:28:28 UTC | a working fix | 27 April 2015, 00:28:28 UTC |
| 45ea02d | Mikhail Kolmogorov | 25 April 2015, 22:54:31 UTC | not going through internal contigs' blocks | 25 April 2015, 22:54:31 UTC |
| 783cbf1 | Mikhail Kolmogorov | 25 April 2015, 21:33:36 UTC | fix for preferred edges heuristic | 25 April 2015, 21:33:36 UTC |
| dc887bc | Mikhail Kolmogorov | 25 April 2015, 21:32:52 UTC | reverted to the original algorithm | 25 April 2015, 21:32:52 UTC |
| 7ac914c | Mikhail Kolmogorov | 25 April 2015, 21:23:27 UTC | somethiing that don't work | 25 April 2015, 21:23:27 UTC |
| a12416b | Mikhail Kolmogorov | 25 April 2015, 20:16:59 UTC | faster version | 25 April 2015, 20:16:59 UTC |
| 6c30aba | Mikhail Kolmogorov | 25 April 2015, 07:17:04 UTC | fixed version | 25 April 2015, 07:17:04 UTC |
| 2f3a02f | Mikhail Kolmogorov | 25 April 2015, 01:51:16 UTC | path covering algorithm | 25 April 2015, 01:51:16 UTC |
| 9f58335 | Mikhail Kolmogorov | 24 April 2015, 01:03:25 UTC | guiding by previous iteration (seems to be not working though) | 24 April 2015, 01:03:25 UTC |
| eda93fd | Mikhail Kolmogorov | 23 April 2015, 23:24:29 UTC | experimental preferred edges selection | 23 April 2015, 23:24:29 UTC |
| c487145 | Mikhail Kolmogorov | 23 April 2015, 21:06:05 UTC | quick fix | 23 April 2015, 21:06:05 UTC |
| bd67ec3 | Mikhail Kolmogorov | 23 April 2015, 20:49:08 UTC | additional logging | 23 April 2015, 20:49:08 UTC |
| 6862b73 | Mikhail Kolmogorov | 23 April 2015, 20:45:44 UTC | Merge branch 'devel' of https://github.com/fenderglass/Ragout into devel | 23 April 2015, 20:45:44 UTC |
| 99b58de | Mikhail Kolmogorov | 14 April 2015, 00:33:38 UTC | maf2synteny updated | 14 April 2015, 00:33:38 UTC |
| d3f213f | Mikhail Kolmogorov | 22 March 2015, 19:11:36 UTC | 1.1 release | 22 March 2015, 19:11:36 UTC |
| 4bf798f | Mikhail Kolmogorov | 22 March 2015, 19:05:32 UTC | chimera detection on by default | 22 March 2015, 19:05:32 UTC |
| 1b87419 | Mikhail Kolmogorov | 20 March 2015, 03:18:59 UTC | no search for chimeras by default, removed debug output | 20 March 2015, 03:18:59 UTC |
| aac094f | Mikhail Kolmogorov | 20 March 2015, 03:13:14 UTC | new config paramter for chimeras | 20 March 2015, 03:13:14 UTC |
| 818acc4 | Mikhail Kolmogorov | 19 March 2015, 03:46:36 UTC | merge | 19 March 2015, 03:46:36 UTC |
| 3349756 | Mikhail Kolmogorov | 19 March 2015, 03:39:11 UTC | more documentation | 19 March 2015, 03:39:11 UTC |
| f90cd91 | Mikhail Kolmogorov | 19 March 2015, 01:31:32 UTC | documentation improved, moving to new release | 19 March 2015, 01:31:32 UTC |
| a010582 | Mikhail Kolmogorov | 18 March 2015, 01:59:36 UTC | non-negative tree lengths, dosumentationimproved | 18 March 2015, 01:59:36 UTC |
| b96240c | Mikhail Kolmogorov | 17 March 2015, 00:37:38 UTC | automatic synteny block scale inference | 17 March 2015, 00:37:38 UTC |
| a2f8861 | Mikhail Kolmogorov | 16 March 2015, 21:38:45 UTC | blocks sizes pre-sets instead of setting them manually | 16 March 2015, 21:38:45 UTC |
| d7eebef | Mikhail Kolmogorov | 13 March 2015, 04:09:52 UTC | Automatic tree inference | 13 March 2015, 04:09:52 UTC |
| 8b3ee82 | Mikhail Kolmogorov | 13 March 2015, 02:59:55 UTC | neighbor-joining algorithm | 13 March 2015, 02:59:55 UTC |
| 54c0ed3 | Mikhail Kolmogorov | 12 March 2015, 04:08:40 UTC | a step towards inferring phylogenetic tree from the data | 12 March 2015, 04:08:40 UTC |
| bd35cb5 | Mikhail Kolmogorov | 05 March 2015, 20:35:08 UTC | added extra condition in split_by_instance | 05 March 2015, 20:35:08 UTC |
| d36d12e | Mikhail Kolmogorov | 04 March 2015, 22:33:27 UTC | small fix in mergin algorithm to prevent scaffolds of length zero | 04 March 2015, 22:33:27 UTC |
| d22c112 | Mikhail Kolmogorov | 04 March 2015, 04:02:22 UTC | logging | 04 March 2015, 04:02:22 UTC |
| f248c08 | Mikhail Kolmogorov | 04 March 2015, 03:59:55 UTC | more smarter and efficient splitting by contig instance algorithm | 04 March 2015, 03:59:55 UTC |
| cda4012 | Mikhail Kolmogorov | 02 March 2015, 03:59:07 UTC | Code cleanup | 02 March 2015, 03:59:07 UTC |
| 1a5aba0 | Mikhail Kolmogorov | 01 March 2015, 23:35:42 UTC | a fix in alignment function + logging | 01 March 2015, 23:35:42 UTC |
| ae22ade | Mikhail Kolmogorov | 28 February 2015, 03:03:31 UTC | couple of fixes in rr | 28 February 2015, 03:03:31 UTC |
| 1b04020 | Mikhail Kolmogorov | 27 February 2015, 22:45:11 UTC | unique and repetitive matches are separated again | 27 February 2015, 22:45:11 UTC |
| c8f031a | Mikhail Kolmogorov | 27 February 2015, 07:50:36 UTC | parsimony test for repeats | 27 February 2015, 07:50:36 UTC |
| 2c43472 | Mikhail Kolmogorov | 26 February 2015, 23:11:51 UTC | building profiles wrt to phylogeny | 26 February 2015, 23:11:51 UTC |
| b9ac97a | Mikhail Kolmogorov | 26 February 2015, 20:56:34 UTC | rr works more or less | 26 February 2015, 20:56:34 UTC |
| 8fdb3eb | Mikhail Kolmogorov | 26 February 2015, 05:08:18 UTC | yet unfinished rr with multiple references | 26 February 2015, 05:08:18 UTC |
| 698d07c | Mikhail Kolmogorov | 26 February 2015, 02:37:48 UTC | resolving repeats in non-repetitive contigs | 26 February 2015, 02:37:48 UTC |
| 0dcd958 | Mikhail Kolmogorov | 26 February 2015, 00:46:45 UTC | Merge branch 'devel' into rr_devel | 26 February 2015, 00:46:45 UTC |
| f069e75 | Mikhail Kolmogorov | 26 February 2015, 00:27:01 UTC | Merge branch 'devel' of https://github.com/fenderglass/Ragout into devel | 26 February 2015, 00:27:01 UTC |
| 65f25fd | Mikhail Kolmogorov | 26 February 2015, 00:19:20 UTC | fix for unspecified branch length + small tree parser reorganization | 26 February 2015, 00:19:20 UTC |
| ba78239 | Mikhail Kolmogorov | 25 February 2015, 23:01:23 UTC | merge | 25 February 2015, 23:01:23 UTC |
| cb29f6a | Mikhail Kolmogorov | 25 February 2015, 22:58:36 UTC | added 2geneorder script, tree branch scaling, void states are free to change, draft references help in chimera filtration | 25 February 2015, 22:58:36 UTC |
| 034e5a8 | Mikhail Kolmogorov | 18 February 2015, 19:49:11 UTC | moving towards rr with multiple references | 18 February 2015, 19:49:11 UTC |
| 2438f90 | Mikhail Kolmogorov | 06 February 2015, 22:19:11 UTC | checking for one reference | 06 February 2015, 22:19:11 UTC |
| 5ee992e | Mikhail Kolmogorov | 03 February 2015, 00:34:19 UTC | oups | 03 February 2015, 00:34:19 UTC |
| 9c667ab | Mikhail Kolmogorov | 02 February 2015, 23:21:36 UTC | fixed errors in merge with repeats | 02 February 2015, 23:21:36 UTC |
| 998b4d1 | Mikhail Kolmogorov | 31 January 2015, 05:31:53 UTC | more conservative distance estimation | 31 January 2015, 05:31:53 UTC |
| 5169de9 | Mikhail Kolmogorov | 28 January 2015, 21:51:39 UTC | fixed bug | 28 January 2015, 21:51:39 UTC |
| 659d98f | Mikahil Kolmogorov | 28 January 2015, 09:21:07 UTC | oups | 28 January 2015, 09:21:07 UTC |
| b92053a | Mikahil Kolmogorov | 28 January 2015, 08:43:50 UTC | fixed distance estimation between contigs | 28 January 2015, 08:43:50 UTC |
| c29dde6 | Mikhail Kolmogorov | 28 January 2015, 03:15:24 UTC | correct version of one-ref repeat resolver | 28 January 2015, 03:15:24 UTC |
| b28a25d | Mikahil Kolmogorov | 27 January 2015, 08:30:16 UTC | moving | 27 January 2015, 08:30:16 UTC |
| ca2df27 | Mikhail Kolmogorov | 27 January 2015, 04:09:45 UTC | hangling repetitive contigs | 27 January 2015, 04:09:45 UTC |
| d9a47f8 | Mikhail Kolmogorov | 27 January 2015, 01:16:52 UTC | some changes | 27 January 2015, 01:16:52 UTC |
| 697e4f6 | Mikhail Kolmogorov | 26 January 2015, 21:50:15 UTC | a fix in rr + command line option | 26 January 2015, 21:50:15 UTC |
| d31b3b8 | Mikhail Kolmogorov | 24 January 2015, 05:03:12 UTC | smarter repeats resoliving | 24 January 2015, 05:03:12 UTC |
| 8fc521b | Mikhail Kolmogorov | 19 January 2015, 21:01:47 UTC | little bit more reliable prediction | 19 January 2015, 21:01:47 UTC |
| 7c89e9e | Mikhail Kolmogorov | 19 January 2015, 20:50:24 UTC | --threads argument, rr disabled | 19 January 2015, 20:50:24 UTC |
