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https://github.com/fenderglass/Ragout
22 June 2021, 01:28:21 UTC
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Revision Author Date Message Commit Date
66138dc fenderglass 21 March 2014, 12:59:50 UTC repo reorganisation 21 March 2014, 12:59:50 UTC
e6e1dd0 fenderglass 20 March 2014, 20:38:01 UTC started repo reorganisation. added overlap sources 20 March 2014, 20:38:01 UTC
e95c01f fenderglass 18 March 2014, 16:53:47 UTC non-recursive overlap graph construction, additional filters for nucmer alignment 18 March 2014, 16:53:47 UTC
cc80639 fenderglass 14 March 2014, 15:50:43 UTC strand checking 14 March 2014, 15:50:43 UTC
ecabefa fenderglass 14 March 2014, 13:29:05 UTC debug output improved 14 March 2014, 13:29:05 UTC
388d840 fenderglass 11 March 2014, 16:10:25 UTC fancy graph pictures 11 March 2014, 16:10:25 UTC
f6ec1fc fenderglass 10 March 2014, 22:55:37 UTC phylogenetic tree output. known edges are added into BG. test script improved a bit 10 March 2014, 22:55:37 UTC
ac511e2 kolmogorov 09 March 2014, 17:15:41 UTC small fix for cactus 09 March 2014, 17:15:41 UTC
c300ebd fenderglass 09 March 2014, 17:14:34 UTC test script changed a bit 09 March 2014, 17:14:34 UTC
44cc310 fenderglass 06 March 2014, 13:02:33 UTC maf2synteny fixes 06 March 2014, 13:02:33 UTC
4ff956e fenderglass 27 February 2014, 10:16:01 UTC reuse of existing sibelia/cacts results 27 February 2014, 10:16:01 UTC
3c35710 fenderglass 26 February 2014, 17:21:39 UTC iterative synteny recovery 26 February 2014, 17:21:39 UTC
1582e4c fenderglass 24 February 2014, 18:30:55 UTC merge with master 24 February 2014, 18:30:55 UTC
aecacb2 fenderglass 24 February 2014, 18:27:34 UTC circular mode 24 February 2014, 18:27:34 UTC
0f746a2 fenderglass 24 February 2014, 17:57:51 UTC finding fragmented synteny blocks 24 February 2014, 17:57:51 UTC
7739e2a fenderglass 18 February 2014, 17:46:26 UTC more accurate bulges removal 18 February 2014, 17:46:26 UTC
bda2b24 fenderglass 17 February 2014, 20:30:10 UTC cactus + syntany backends 17 February 2014, 20:30:10 UTC
67c4322 fenderglass 14 February 2014, 15:25:38 UTC adhoc fixes for bulge removal 14 February 2014, 15:25:38 UTC
bf8bba8 fenderglass 13 February 2014, 15:04:48 UTC small fix 13 February 2014, 15:04:48 UTC
d8f37bd fenderglass 13 February 2014, 14:49:56 UTC merge 13 February 2014, 14:49:56 UTC
6dc4c93 fenderglass 13 February 2014, 14:41:24 UTC reorganization 13 February 2014, 14:41:24 UTC
519f811 fenderglass 13 February 2014, 14:38:08 UTC bulges removal 13 February 2014, 14:38:08 UTC
4a6d289 fenderglass 12 February 2014, 15:32:49 UTC bulges 12 February 2014, 15:32:49 UTC
97487aa fenderglass 12 February 2014, 12:10:36 UTC another fix 12 February 2014, 12:10:36 UTC
2260cda fenderglass 12 February 2014, 12:09:32 UTC usage fix 12 February 2014, 12:09:32 UTC
4633c80 fenderglass 12 February 2014, 12:07:39 UTC standalone installer 12 February 2014, 12:07:39 UTC
88b01f9 fenderglass 11 February 2014, 17:02:24 UTC Sibelia installer 11 February 2014, 17:02:24 UTC
d6a6f4f fenderglass 11 February 2014, 15:42:29 UTC minor change 11 February 2014, 15:42:29 UTC
a49a37b fenderglass 11 February 2014, 13:22:19 UTC maf alignment filtering 11 February 2014, 13:22:19 UTC
36ba067 fenderglass 10 February 2014, 15:03:23 UTC coordinates tracking changed 10 February 2014, 15:03:23 UTC
16044a1 fenderglass 07 February 2014, 15:28:58 UTC some changes 07 February 2014, 15:28:58 UTC
01df032 fenderglass 06 February 2014, 19:41:29 UTC docs 06 February 2014, 19:41:29 UTC
9d2077f fenderglass 06 February 2014, 16:40:18 UTC fixed bug with tandem repeat 06 February 2014, 16:40:18 UTC
dd77e07 fenderglass 05 February 2014, 15:25:22 UTC maf2synteny 05 February 2014, 15:25:22 UTC
a976466 fenderglass 04 February 2014, 15:56:05 UTC lcb generation scripts 04 February 2014, 15:56:05 UTC
43c1081 fenderglass 29 January 2014, 11:28:29 UTC comments in code 29 January 2014, 11:28:29 UTC
5818c57 fenderglass 19 January 2014, 08:12:23 UTC supplementary update 19 January 2014, 08:12:23 UTC
e438e71 fenderglass 16 January 2014, 11:06:32 UTC ismb2014 16 January 2014, 11:06:32 UTC
54ec831 fenderglass 15 January 2014, 22:20:24 UTC sibelia path fix 15 January 2014, 22:20:24 UTC
b0a0b5a fenderglass 14 January 2014, 10:44:45 UTC small usage update 14 January 2014, 10:44:45 UTC
2e5adc7 fenderglass 14 January 2014, 09:53:13 UTC install and usage 14 January 2014, 09:53:13 UTC
c700bcf fenderglass 14 January 2014, 08:46:45 UTC readme 14 January 2014, 08:46:45 UTC
43b5052 fenderglass 04 January 2014, 14:37:47 UTC optimization 04 January 2014, 14:37:47 UTC
a52dcb8 fenderglass 04 January 2014, 11:30:48 UTC more accurate handling of known adjacencies 04 January 2014, 11:30:48 UTC
fac714c fenderglass 25 December 2013, 15:44:43 UTC small fix 25 December 2013, 15:44:43 UTC
b9ad65b fenderglass 19 December 2013, 15:26:25 UTC test script updated, new coord files 19 December 2013, 15:26:25 UTC
6a6951c fenderglass 11 December 2013, 14:17:17 UTC bugfixes in assembly graph 11 December 2013, 14:17:17 UTC
313f6be fenderglass 09 December 2013, 17:58:22 UTC examples fixed 09 December 2013, 17:58:22 UTC
ccf92fa fenderglass 09 December 2013, 15:12:08 UTC small ifx 09 December 2013, 15:12:08 UTC
e2345a4 fenderglass 26 November 2013, 15:39:10 UTC some logging 26 November 2013, 15:39:10 UTC
ab25327 fenderglass 26 November 2013, 13:40:46 UTC more reliable parsers 26 November 2013, 13:40:46 UTC
db29c03 fenderglass 21 November 2013, 12:31:54 UTC new dot parser + nucmer format fixes 21 November 2013, 12:31:54 UTC
d7ca7ca fenderglass 18 November 2013, 20:54:54 UTC usage og known adjacencies 18 November 2013, 20:54:54 UTC
b178423 fenderglass 18 November 2013, 14:04:20 UTC USAGE improved 18 November 2013, 14:04:20 UTC
0c5e62d fenderglass 18 November 2013, 13:39:32 UTC new example 18 November 2013, 13:39:32 UTC
7ff9793 fenderglass 18 November 2013, 13:30:30 UTC sankoff algorithm 18 November 2013, 13:30:30 UTC
c5e68c1 fenderglass 18 November 2013, 11:16:35 UTC new script 18 November 2013, 11:16:35 UTC
3a9fa50 fenderglass 18 November 2013, 11:14:53 UTC aureus config fix 18 November 2013, 11:14:53 UTC
9808b68 fenderglass 12 November 2013, 13:14:42 UTC fixed example configs 12 November 2013, 13:14:42 UTC
a599a30 fenderglass 11 November 2013, 11:43:38 UTC fixed huge phylogeny bugs 11 November 2013, 11:43:38 UTC
4cb0fea fenderglass 11 November 2013, 00:00:51 UTC debug output 11 November 2013, 00:00:51 UTC
a020c19 fenderglass 07 November 2013, 14:05:09 UTC debrujin refinement 07 November 2013, 14:05:09 UTC
e54c487 fenderglass 06 November 2013, 22:56:35 UTC test script with multiple references 06 November 2013, 22:56:35 UTC
b190ee0 Nikolay Vyahhi 06 November 2013, 21:32:28 UTC Python 2.6 minor. 06 November 2013, 21:32:28 UTC
1bca0a3 Nikolay Vyahhi 06 November 2013, 21:18:21 UTC Usage minor. 06 November 2013, 21:18:21 UTC
f2c9868 Nikolay Vyahhi 06 November 2013, 21:17:33 UTC Applying markdown to readme files. 06 November 2013, 21:17:33 UTC
5e574e7 Nikolay Vyahhi 06 November 2013, 21:14:30 UTC README improvements. 06 November 2013, 21:16:20 UTC
7d6d083 Nikolay Vyahhi 06 November 2013, 20:53:41 UTC Update USAGE 06 November 2013, 20:53:41 UTC
f627e95 fenderglass 06 November 2013, 06:54:02 UTC small ifx 06 November 2013, 06:54:02 UTC
3efaa2e fenderglass 05 November 2013, 19:47:36 UTC output dirs 05 November 2013, 19:47:36 UTC
e1a5b7f fenderglass 05 November 2013, 19:45:23 UTC readme and examples added 05 November 2013, 19:45:23 UTC
ef9c7dd fenderglass 04 November 2013, 21:51:37 UTC minor fix 04 November 2013, 21:51:37 UTC
eed23ae fenderglass 04 November 2013, 21:48:47 UTC fasta output 04 November 2013, 21:48:47 UTC
9391e37 fenderglass 02 November 2013, 21:15:54 UTC iterative 02 November 2013, 21:15:54 UTC
514db70 fenderglass 02 November 2013, 10:39:43 UTC sibelia incorporated 02 November 2013, 10:39:43 UTC
3b1aacc fenderglass 01 November 2013, 15:54:36 UTC it works with permutations 01 November 2013, 15:54:36 UTC
ecc22e8 fenderglass 01 November 2013, 15:03:50 UTC continue refactoring 01 November 2013, 15:03:50 UTC
aa2d169 fenderglass 31 October 2013, 20:20:11 UTC BG with permutations 31 October 2013, 20:20:11 UTC
abb3b63 fenderglass 31 October 2013, 16:02:29 UTC new branch 31 October 2013, 16:02:29 UTC
23789cd fenderglass 31 October 2013, 16:00:38 UTC slight refactoring 31 October 2013, 16:00:38 UTC
25d3aee fenderglass 30 October 2013, 08:24:06 UTC Merge branch 'master' of github.com:fenderglass/refass 30 October 2013, 08:24:06 UTC
b54f17e fenderglass 30 October 2013, 08:23:59 UTC minor change 30 October 2013, 08:23:59 UTC
9c6e26c fenderglass 28 October 2013, 15:34:19 UTC refactoring 28 October 2013, 15:34:19 UTC
9214e85 fenderglass 19 October 2013, 22:10:10 UTC Automatic testing 19 October 2013, 22:10:10 UTC
2c683c8 fenderglass 17 October 2013, 13:45:12 UTC with debrujin refinement 17 October 2013, 13:45:12 UTC
b853b4e fenderglass 17 October 2013, 13:14:06 UTC new iterative assembly 17 October 2013, 13:14:06 UTC
ac49d14 fenderglass 07 October 2013, 17:47:42 UTC partitoning algorithms improved 07 October 2013, 17:47:42 UTC
5fe6d4c fenderglass 06 October 2013, 15:41:03 UTC Super rearrangement simpulator 2000 06 October 2013, 15:41:03 UTC
0e89949 fenderglass 04 October 2013, 15:25:26 UTC splitting genomes into blocks 04 October 2013, 15:25:26 UTC
c2a27d4 fenderglass 02 October 2013, 20:12:07 UTC more fancy images 02 October 2013, 20:12:07 UTC
157f93f fenderglass 30 September 2013, 22:09:02 UTC phylogeny incorporated 30 September 2013, 22:09:02 UTC
f3ec594 fenderglass 30 September 2013, 11:26:20 UTC quick and dirty phylogeny 30 September 2013, 11:26:20 UTC
270c4d9 fenderglass 30 September 2013, 09:46:58 UTC phylogenetic trees likelihood estimation 30 September 2013, 09:46:58 UTC
f6de2c5 fenderglass 16 September 2013, 22:39:39 UTC matching graph partitioning 16 September 2013, 22:39:39 UTC
3e5d161 fenderglass 30 August 2013, 14:25:38 UTC breakpoint graph refactoring 30 August 2013, 14:25:38 UTC
a13a487 fenderglass 29 August 2013, 11:44:22 UTC something changed 29 August 2013, 11:44:22 UTC
4cb396a fenderglass 28 August 2013, 12:23:48 UTC debrujin integration, interface changed 28 August 2013, 12:23:48 UTC
12a2258 fenderglass 26 August 2013, 14:39:52 UTC bugfix and skipping missing blocks, when constructing bg 26 August 2013, 14:39:52 UTC
22d1a57 fenderglass 24 August 2013, 09:31:41 UTC overlap graph building and checking 24 August 2013, 09:31:41 UTC
3d0c999 fenderglass 23 August 2013, 15:37:07 UTC more accurate test (not automatical yet) 23 August 2013, 15:37:07 UTC
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