https://github.com/fenderglass/Ragout

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Revision Author Date Message Commit Date
4b42dde instal 26 April 2014, 05:29:56 UTC
c88cc53 docs updated 26 April 2014, 05:18:40 UTC
b9c0c95 oups 17 April 2014, 12:48:24 UTC
fb0a2ea cross-ilnks 17 April 2014, 12:47:54 UTC
6e2322e added link to install-sibelia.py 17 April 2014, 11:45:31 UTC
78d31da uploading to PyPI 17 April 2014, 11:35:23 UTC
89136a4 added setuptools bootstrap, installation script improved 17 April 2014, 09:34:17 UTC
fbf60af oups 16 April 2014, 15:20:14 UTC
0feea83 compilation under gcc46 16 April 2014, 15:18:29 UTC
4a5248c some fixes 16 April 2014, 12:39:29 UTC
2ae2282 v0.2b 15 April 2014, 15:09:40 UTC
15e9dbf removed deprecated code 15 April 2014, 14:18:41 UTC
0672c97 inplace usage option 15 April 2014, 12:18:59 UTC
368a7d8 package fix 15 April 2014, 10:49:28 UTC
fc81a29 python package 14 April 2014, 20:38:07 UTC
fe7d04c c++ extensions catch Ctr-C; an attemt to create setup script 14 April 2014, 17:10:42 UTC
1491a04 example changed, sibelia now works with --fine 12 April 2014, 09:27:59 UTC
ff62ec1 exiting on error in synteny backend 10 April 2014, 15:09:57 UTC
07f50cb more pretty makefile 08 April 2014, 18:07:03 UTC
7880dfe manuals updated 08 April 2014, 17:53:41 UTC
8076599 checking python version 08 April 2014, 17:19:32 UTC
ab7b582 scripts now supports both 2 and 3 python version 08 April 2014, 16:45:03 UTC
1fbdc34 one more fix for c++0x 08 April 2014, 08:40:05 UTC
c29e7af fix for cmpilation under gcc4.6 + usage updated 08 April 2014, 08:23:30 UTC
ff7da05 cpp maf2synteny implementation incorporated + some fixes inside 07 April 2014, 17:00:16 UTC
6d64e70 maf2synteny speedup, memory leaks fixed 03 April 2014, 21:18:57 UTC
f2b439e parameter fixes 01 April 2014, 16:42:18 UTC
feaa357 interpreter changed to python2 01 April 2014, 16:09:22 UTC
14d5993 some backported things 01 April 2014, 16:08:39 UTC
41974d7 maf2synteny finally works 01 April 2014, 16:08:12 UTC
915d1d1 rewritten 31 March 2014, 17:23:59 UTC
a95bc0e path compression and bulge removal seems to be working 28 March 2014, 17:09:05 UTC
d3368d3 maf parser partially implemented 26 March 2014, 14:50:15 UTC
298d2be compression algorithms in c++ 26 March 2014, 13:26:12 UTC
ab795cc started porting maf2synteny on c++ 25 March 2014, 17:03:08 UTC
c4d61e9 more refactoring 24 March 2014, 12:24:02 UTC
89ed1ad small fix 21 March 2014, 15:59:11 UTC
be3a049 ovelap tools as .so library. incorporated into pipeline 21 March 2014, 15:34:21 UTC
66138dc repo reorganisation 21 March 2014, 12:59:50 UTC
e6e1dd0 started repo reorganisation. added overlap sources 20 March 2014, 20:38:01 UTC
e95c01f non-recursive overlap graph construction, additional filters for nucmer alignment 18 March 2014, 16:53:47 UTC
cc80639 strand checking 14 March 2014, 15:50:43 UTC
ecabefa debug output improved 14 March 2014, 13:29:05 UTC
388d840 fancy graph pictures 11 March 2014, 16:10:25 UTC
f6ec1fc phylogenetic tree output. known edges are added into BG. test script improved a bit 10 March 2014, 22:55:37 UTC
ac511e2 small fix for cactus 09 March 2014, 17:15:41 UTC
c300ebd test script changed a bit 09 March 2014, 17:14:34 UTC
44cc310 maf2synteny fixes 06 March 2014, 13:02:33 UTC
4ff956e reuse of existing sibelia/cacts results 27 February 2014, 10:16:01 UTC
3c35710 iterative synteny recovery 26 February 2014, 17:21:39 UTC
1582e4c merge with master 24 February 2014, 18:30:55 UTC
aecacb2 circular mode 24 February 2014, 18:27:34 UTC
0f746a2 finding fragmented synteny blocks 24 February 2014, 17:57:51 UTC
7739e2a more accurate bulges removal 18 February 2014, 17:46:26 UTC
bda2b24 cactus + syntany backends 17 February 2014, 20:30:10 UTC
67c4322 adhoc fixes for bulge removal 14 February 2014, 15:25:38 UTC
bf8bba8 small fix 13 February 2014, 15:04:48 UTC
d8f37bd merge 13 February 2014, 14:49:56 UTC
6dc4c93 reorganization 13 February 2014, 14:41:24 UTC
519f811 bulges removal 13 February 2014, 14:38:08 UTC
4a6d289 bulges 12 February 2014, 15:32:49 UTC
97487aa another fix 12 February 2014, 12:10:36 UTC
2260cda usage fix 12 February 2014, 12:09:32 UTC
4633c80 standalone installer 12 February 2014, 12:07:39 UTC
88b01f9 Sibelia installer 11 February 2014, 17:02:24 UTC
d6a6f4f minor change 11 February 2014, 15:42:29 UTC
a49a37b maf alignment filtering 11 February 2014, 13:22:19 UTC
36ba067 coordinates tracking changed 10 February 2014, 15:03:23 UTC
16044a1 some changes 07 February 2014, 15:28:58 UTC
01df032 docs 06 February 2014, 19:41:29 UTC
9d2077f fixed bug with tandem repeat 06 February 2014, 16:40:18 UTC
dd77e07 maf2synteny 05 February 2014, 15:25:22 UTC
a976466 lcb generation scripts 04 February 2014, 15:56:05 UTC
43c1081 comments in code 29 January 2014, 11:28:29 UTC
5818c57 supplementary update 19 January 2014, 08:12:23 UTC
e438e71 ismb2014 16 January 2014, 11:06:32 UTC
54ec831 sibelia path fix 15 January 2014, 22:20:24 UTC
b0a0b5a small usage update 14 January 2014, 10:44:45 UTC
2e5adc7 install and usage 14 January 2014, 09:53:13 UTC
c700bcf readme 14 January 2014, 08:46:45 UTC
43b5052 optimization 04 January 2014, 14:37:47 UTC
a52dcb8 more accurate handling of known adjacencies 04 January 2014, 11:30:48 UTC
fac714c small fix 25 December 2013, 15:44:43 UTC
b9ad65b test script updated, new coord files 19 December 2013, 15:26:25 UTC
6a6951c bugfixes in assembly graph 11 December 2013, 14:17:17 UTC
313f6be examples fixed 09 December 2013, 17:58:22 UTC
ccf92fa small ifx 09 December 2013, 15:12:08 UTC
e2345a4 some logging 26 November 2013, 15:39:10 UTC
ab25327 more reliable parsers 26 November 2013, 13:40:46 UTC
db29c03 new dot parser + nucmer format fixes 21 November 2013, 12:31:54 UTC
d7ca7ca usage og known adjacencies 18 November 2013, 20:54:54 UTC
b178423 USAGE improved 18 November 2013, 14:04:20 UTC
0c5e62d new example 18 November 2013, 13:39:32 UTC
7ff9793 sankoff algorithm 18 November 2013, 13:30:30 UTC
c5e68c1 new script 18 November 2013, 11:16:35 UTC
3a9fa50 aureus config fix 18 November 2013, 11:14:53 UTC
9808b68 fixed example configs 12 November 2013, 13:14:42 UTC
a599a30 fixed huge phylogeny bugs 11 November 2013, 11:43:38 UTC
4cb0fea debug output 11 November 2013, 00:00:51 UTC
a020c19 debrujin refinement 07 November 2013, 14:05:09 UTC
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