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 |
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 |
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 |
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 |
0498a1b | Mikhail Kolmogorov | 17 January 2015, 02:36:08 UTC | probably correct rr | 17 January 2015, 02:36:08 UTC |
1dc768d | Mikhail Kolmogorov | 17 January 2015, 01:41:16 UTC | two bugfixes | 17 January 2015, 01:41:16 UTC |
1c57a3d | Mikhail Kolmogorov | 16 January 2015, 03:52:51 UTC | rr improved a bit | 16 January 2015, 03:52:51 UTC |
d21ab39 | Mikhail Kolmogorov | 16 January 2015, 00:58:05 UTC | an initial repeat resolver | 16 January 2015, 00:58:05 UTC |
ebb76de | Mikhail Kolmogorov | 15 January 2015, 20:42:29 UTC | small bug in merging | 15 January 2015, 20:42:29 UTC |
ebd560a | Mikhail Kolmogorov | 15 January 2015, 05:07:44 UTC | merging procedure handles repeats | 15 January 2015, 05:07:44 UTC |
9461555 | Mikhail Kolmogorov | 15 January 2015, 01:42:43 UTC | more necessary refactoring | 15 January 2015, 01:42:43 UTC |
44f0be6 | Mikhail Kolmogorov | 15 January 2015, 00:13:06 UTC | fixed error | 15 January 2015, 00:13:06 UTC |
7312b50 | Mikhail Kolmogorov | 15 January 2015, 00:01:54 UTC | preparing to big changes | 15 January 2015, 00:01:54 UTC |
e508020 | Mikhail Kolmogorov | 12 January 2015, 22:31:37 UTC | a possible fix for fusion prediction | 12 January 2015, 22:31:37 UTC |
55f7171 | Mikhail Kolmogorov | 12 January 2015, 22:19:06 UTC | refactoring | 12 January 2015, 22:19:06 UTC |
4510624 | Mikhail Kolmogorov | 08 January 2015, 00:13:40 UTC | fix in hal2fasta + conservative chimera again + fix in recipe parsing | 08 January 2015, 00:13:40 UTC |
ff076b8 | Mikhail Kolmogorov | 07 January 2015, 00:59:01 UTC | Merge branch 'devel' of github.com:fenderglass/Ragout into devel | 07 January 2015, 00:59:01 UTC |
793f7cb | Mikhail Kolmogorov | 07 January 2015, 00:58:50 UTC | bugfix | 07 January 2015, 00:58:50 UTC |
0a1595e | fenderglass | 06 January 2015, 22:37:50 UTC | minor fix | 06 January 2015, 22:37:50 UTC |
20ab4d5 | Mikhail Kolmogorov | 06 January 2015, 20:58:36 UTC | fasta from hal | 06 January 2015, 20:58:36 UTC |
f786d0a | Mikhail Kolmogorov | 06 January 2015, 05:55:40 UTC | hal backend | 06 January 2015, 05:55:40 UTC |
83c65dc | Mikhail Kolmogorov | 29 December 2014, 02:21:02 UTC | more smart prediction | 29 December 2014, 02:21:02 UTC |
b8d4735 | Mikhail Kolmogorov | 28 December 2014, 08:40:02 UTC | preditcion back on | 28 December 2014, 08:40:02 UTC |
02755e9 | Mikhail Kolmogorov | 24 December 2014, 23:22:25 UTC | little bit different chimera handling | 24 December 2014, 23:22:25 UTC |
8956979 | Mikhail Kolmogorov | 23 December 2014, 07:22:30 UTC | more precise chimera detection | 23 December 2014, 07:22:30 UTC |
7ebb89c | Mikhail Kolmogorov | 23 December 2014, 01:33:42 UTC | bottleneck fixed | 23 December 2014, 01:33:42 UTC |
4a9a30e | Mikhail Kolmogorov | 22 December 2014, 21:29:38 UTC | couple of small fixes | 22 December 2014, 21:29:38 UTC |
ee856b2 | Mikhail Kolmogorov | 22 December 2014, 21:12:46 UTC | chimeras detection, some refactoring | 22 December 2014, 21:12:46 UTC |
fc2be5e | Mikhail Kolmogorov | 22 December 2014, 01:38:14 UTC | experimental anti-fusion version | 22 December 2014, 01:38:14 UTC |
3dc894c | Mikhail Kolmogorov | 18 December 2014, 02:16:09 UTC | joiin_collinear rewritten | 18 December 2014, 02:16:09 UTC |
8f9f473 | Mikhail Kolmogorov | 11 December 2014, 23:09:49 UTC | nochain | 11 December 2014, 23:09:49 UTC |
fded228 | Mikhail Kolmogorov | 09 December 2014, 18:56:10 UTC | rearrangement prediction turned off | 09 December 2014, 18:56:10 UTC |
209625f | Mikhail Kolmogorov | 04 December 2014, 01:15:59 UTC | block parameter added | 04 December 2014, 01:15:59 UTC |
96c1e1e | Mikhail Kolmogorov | 04 December 2014, 01:11:43 UTC | rest scripts moved to right alignmet format | 04 December 2014, 01:11:43 UTC |
a329583 | Mikhail Kolmogorov | 04 December 2014, 00:32:46 UTC | comparison script works better, new alignment representation | 04 December 2014, 00:32:46 UTC |
f0f6978 | Mikhail Kolmogorov | 02 December 2014, 02:56:34 UTC | more refactoring | 02 December 2014, 02:56:34 UTC |
5dbbb3f | Mikhail Kolmogorov | 02 December 2014, 02:43:34 UTC | new version of assemblies comparison script + refactoring | 02 December 2014, 02:43:34 UTC |
0fc9eb6 | Mikhail Kolmogorov | 01 December 2014, 21:56:05 UTC | Merge branch 'devel' of github.com:fenderglass/Ragout into devel | 01 December 2014, 21:56:05 UTC |
3fb655d | Mikhail Kolmogorov | 01 December 2014, 21:55:58 UTC | file mode change | 01 December 2014, 21:55:58 UTC |
cbe8347 | Mikhail Kolmogorov | 01 December 2014, 17:25:30 UTC | something changed | 01 December 2014, 17:25:30 UTC |
7a357f7 | Mikhail Kolmogorov | 30 November 2014, 22:40:16 UTC | a script for comparing two assemblies | 30 November 2014, 22:40:16 UTC |
777eb5f | fenderglass | 01 November 2014, 01:04:10 UTC | fixed tilde recognition in config paths, tree parser now accepts float values in exp format | 01 November 2014, 01:04:10 UTC |
c5d640c | fenderglass | 17 October 2014, 22:22:20 UTC | copyright notice fo scripts | 17 October 2014, 22:22:20 UTC |
2a52465 | fenderglass | 30 September 2014, 22:07:28 UTC | added two scripts, help improved | 30 September 2014, 22:07:28 UTC |
4ed9f44 | fenderglass | 11 September 2014, 16:49:59 UTC | ambigious fasta characters | 11 September 2014, 16:49:59 UTC |
d599412 | fenderglass | 11 September 2014, 12:32:00 UTC | verification script supports both links and ord format | 11 September 2014, 12:32:00 UTC |
51c9f86 | fenderglass | 25 August 2014, 10:33:31 UTC | capturing output of native modules, logging improved | 25 August 2014, 10:33:31 UTC |
d919fa0 | fenderglass | 24 August 2014, 18:46:26 UTC | --hist option in overlap module | 24 August 2014, 18:46:26 UTC |
9a821fa | fenderglass | 12 August 2014, 15:04:58 UTC | error message fix | 12 August 2014, 15:04:58 UTC |
4011904 | fenderglass | 08 August 2014, 06:20:32 UTC | version 1.0 | 08 August 2014, 06:20:32 UTC |
5783aa3 | fenderglass | 07 August 2014, 19:31:39 UTC | minor logging improvement | 07 August 2014, 19:31:39 UTC |
4c47ee5 | fenderglass | 07 August 2014, 19:06:52 UTC | refine by default, additinal testing for native modules | 07 August 2014, 19:06:52 UTC |
8cdb83e | fenderglass | 07 August 2014, 09:29:42 UTC | refinement added to tests | 07 August 2014, 09:29:42 UTC |
c09edca | fenderglass | 07 August 2014, 09:06:56 UTC | changed rows order in links file, debug output improved | 07 August 2014, 09:06:56 UTC |
e0a19b4 | fenderglass | 06 August 2014, 18:23:39 UTC | small improvement in refinement | 06 August 2014, 18:23:39 UTC |
5cfb484 | fenderglass | 30 July 2014, 18:23:05 UTC | faster cut vertex algorithm, fixed bug with debug | 30 July 2014, 18:23:05 UTC |
f7a3a1f | fenderglass | 22 July 2014, 17:04:18 UTC | more pretty links, ord removed | 22 July 2014, 17:04:18 UTC |
340a0ea | fenderglass | 21 July 2014, 15:32:55 UTC | links output format slightly changed | 21 July 2014, 15:32:55 UTC |
2b0ae81 | fenderglass | 21 July 2014, 14:45:33 UTC | Merge branch 'lanna' of github.com:fenderglass/Ragout into devel | 21 July 2014, 14:45:33 UTC |
94082c3 | fenderglass | 21 July 2014, 12:53:51 UTC | example typo | 21 July 2014, 12:53:51 UTC |