| f9920eb | andrewjpage | 29 June 2015, 15:47:04 UTC | use fastml module for script and print message with model and version used | 29 June 2015, 15:47:04 UTC |
| 17070e5 | andrewjpage | 29 June 2015, 15:40:43 UTC | detect custom fastml2 | 29 June 2015, 15:40:43 UTC |
| e4f2d25 | andrewjpage | 29 June 2015, 15:16:50 UTC | detect fastml2 | 29 June 2015, 15:16:50 UTC |
| 24d1d5a | andrewjpage | 29 June 2015, 15:10:47 UTC | detect version | 29 June 2015, 15:10:47 UTC |
| 33ff6b5 | andrewjpage | 29 June 2015, 14:49:55 UTC | new Fastml file | 29 June 2015, 14:49:55 UTC |
| 7127437 | andrewjpage | 29 June 2015, 14:49:19 UTC | rename fastml | 29 June 2015, 14:49:19 UTC |
| 31fb9db | andrewjpage | 29 June 2015, 14:44:45 UTC | update namespace | 29 June 2015, 14:44:45 UTC |
| 4de3d8b | andrewjpage | 29 June 2015, 14:26:48 UTC | initial tests for fastml detection | 29 June 2015, 14:26:48 UTC |
| a866ff1 | andrewjpage | 29 June 2015, 14:26:11 UTC | python3 in shebang | 29 June 2015, 14:26:11 UTC |
| 4278a33 | andrewjpage | 29 June 2015, 11:04:43 UTC | python3 for travis | 29 June 2015, 11:04:43 UTC |
| c89fd89 | andrewjpage | 29 June 2015, 10:13:34 UTC | install setuptools package | 29 June 2015, 10:13:34 UTC |
| ed7b41c | andrewjpage | 29 June 2015, 10:05:37 UTC | temp remove broken install commands | 29 June 2015, 10:05:37 UTC |
| e6b1b44 | andrewjpage | 29 June 2015, 10:05:01 UTC | require a higher version of setuptools | 29 June 2015, 10:05:01 UTC |
| 927ae07 | andrewjpage | 29 June 2015, 09:03:11 UTC | set defaults for input flags | 29 June 2015, 09:03:11 UTC |
| 6b4c138 | andrewjpage | 29 June 2015, 08:19:51 UTC | c warnings about fgets return var and libtool for vagrant | 29 June 2015, 08:19:51 UTC |
| 0f9258a | andrewjpage | 29 June 2015, 08:13:28 UTC | python3 in configure | 29 June 2015, 08:13:28 UTC |
| 3cfadc1 | andrewjpage | 26 June 2015, 15:24:57 UTC | update install docs and build env | 26 June 2015, 15:24:57 UTC |
| 7aa7563 | andrewjpage | 26 June 2015, 15:17:21 UTC | test data update | 26 June 2015, 15:17:21 UTC |
| c4132d4 | andrewjpage | 26 June 2015, 15:07:54 UTC | non bi tree output updated | 26 June 2015, 15:07:54 UTC |
| cad4223 | andrewjpage | 26 June 2015, 14:51:19 UTC | updated test output | 26 June 2015, 14:51:19 UTC |
| 8eaa265 | andrewjpage | 26 June 2015, 14:36:50 UTC | remove outdegree | 26 June 2015, 14:36:50 UTC |
| c6454c3 | andrewjpage | 26 June 2015, 14:35:03 UTC | update splits | 26 June 2015, 14:35:03 UTC |
| 86fee23 | andrewjpage | 26 June 2015, 14:27:43 UTC | fix file opening | 26 June 2015, 14:27:43 UTC |
| 9276e70 | andrewjpage | 26 June 2015, 14:11:45 UTC | remove deprecated U | 26 June 2015, 14:11:45 UTC |
| cf0ebf4 | andrewjpage | 26 June 2015, 14:07:19 UTC | close file handles | 26 June 2015, 14:07:19 UTC |
| cd33a69 | andrewjpage | 26 June 2015, 13:40:24 UTC | convert more comparisions to filecmp | 26 June 2015, 13:40:24 UTC |
| 4e8ae80 | andrewjpage | 26 June 2015, 13:37:37 UTC | use file compare | 26 June 2015, 13:37:37 UTC |
| 4288856 | andrewjpage | 26 June 2015, 12:58:30 UTC | file open | 26 June 2015, 12:58:30 UTC |
| 4719b05 | andrewjpage | 26 June 2015, 12:44:41 UTC | new tree compare syntax | 26 June 2015, 12:44:41 UTC |
| 3bae85f | andrewjpage | 26 June 2015, 12:29:31 UTC | latest version of dendropy | 26 June 2015, 12:29:31 UTC |
| 3202a48 | andrewjpage | 26 June 2015, 12:27:34 UTC | set schema | 26 June 2015, 12:27:34 UTC |
| bed7256 | andrewjpage | 26 June 2015, 11:57:26 UTC | 2to3 python converter script | 26 June 2015, 11:57:26 UTC |
| 1730436 | andrewjpage | 11 June 2015, 14:10:29 UTC | Merge branch 'raxml_version_travis' | 11 June 2015, 14:10:29 UTC |
| 3f41db0 | andrewjpage | 11 June 2015, 14:10:09 UTC | update travis image | 11 June 2015, 14:10:09 UTC |
| be8089d | andrewjpage | 11 June 2015, 14:08:47 UTC | update raxml version for travis | 11 June 2015, 14:08:47 UTC |
| 9695a3d | andrewjpage | 11 June 2015, 14:08:28 UTC | Merge pull request #148 from andrewjpage/raxml_version_travis update raxml version for travis | 11 June 2015, 14:08:28 UTC |
| c34f5b4 | John Tate | 04 June 2015, 14:42:02 UTC | Merge pull request #147 from sanger-pathogens/travis Add build status to README | 04 June 2015, 14:42:02 UTC |
| fbd0c5e | Ben Taylor | 04 June 2015, 13:52:22 UTC | Add build status to README | 04 June 2015, 13:52:22 UTC |
| eb0c72b | John Tate | 04 June 2015, 13:31:50 UTC | Merge pull request #146 from sanger-pathogens/travis Add TravisCI support | 04 June 2015, 13:31:50 UTC |
| 9e38a6e | Ben Taylor | 04 June 2015, 13:16:00 UTC | Add .travis.yml for TravisCI | 04 June 2015, 13:16:00 UTC |
| 39c10df | Ben Taylor | 04 June 2015, 09:57:57 UTC | Add install_dependencies for TravisCI | 04 June 2015, 13:15:40 UTC |
| 1278cca | Ben Taylor | 28 May 2015, 15:25:55 UTC | Merge pull request #145 from aslett1/master Reference URL updated to final published version not early access | 28 May 2015, 15:25:55 UTC |
| 3cfd8c8 | Martin Aslett | 28 May 2015, 14:56:24 UTC | Reference URL updated to final published version not early access | 28 May 2015, 14:56:24 UTC |
| bc8d0ff | andrewjpage | 19 May 2015, 13:22:29 UTC | Merge branch 'master' of github.com:sanger-pathogens/gubbins | 19 May 2015, 13:22:29 UTC |
| eb2494f | andrewjpage | 19 May 2015, 13:22:07 UTC | use fastml3 | 19 May 2015, 13:22:07 UTC |
| 9a5e985 | andrewjpage | 18 May 2015, 14:21:59 UTC | Merge pull request #144 from andrewjpage/master Manually merge Aidan Delaneys pull request | 18 May 2015, 14:21:59 UTC |
| cf0d8a7 | andrewjpage | 18 May 2015, 14:21:21 UTC | Merge branch 'master' of github.com:sanger-pathogens/gubbins | 18 May 2015, 14:21:21 UTC |
| c9276d1 | andrewjpage | 18 May 2015, 14:20:20 UTC | install md | 18 May 2015, 14:20:20 UTC |
| c055bdf | andrewjpage | 18 May 2015, 14:19:37 UTC | Merge branch 'AidanDelaney-master' | 18 May 2015, 14:19:37 UTC |
| bffe70c | martinghunt | 18 May 2015, 14:14:16 UTC | Merge pull request #143 from andrewjpage/recombinations_at_root Detect blocks at end of sequence | 18 May 2015, 14:14:16 UTC |
| 9794732 | andrewjpage | 18 May 2015, 13:51:49 UTC | changelog | 18 May 2015, 13:51:49 UTC |
| afb6460 | andrewjpage | 18 May 2015, 13:50:03 UTC | inc version | 18 May 2015, 13:50:03 UTC |
| 75ebfd5 | andrewjpage | 18 May 2015, 13:45:34 UTC | close a block at the end of the genome | 18 May 2015, 13:49:28 UTC |
| ef7e20a | andrewjpage | 18 May 2015, 13:10:50 UTC | test to replicate bad data | 18 May 2015, 13:10:50 UTC |
| 3e7a7ce | andrewjpage | 15 May 2015, 10:49:54 UTC | display install file as markdown | 15 May 2015, 10:49:54 UTC |
| bc4edbc | andrewjpage | 15 May 2015, 08:49:32 UTC | tab between cells in stats | 15 May 2015, 08:49:32 UTC |
| a121363 | Aidan Delaney | 20 April 2015, 19:24:42 UTC | Updated documentation to fix Issue #130 - documentation should make it clear to run autoreconf before configure. | 20 April 2015, 19:24:42 UTC |
| 17c4924 | Aidan Delaney | 20 April 2015, 19:19:35 UTC | This time with valid URL for updated gubbins package. | 20 April 2015, 19:19:35 UTC |
| 98cf1bf | Aidan Delaney | 20 April 2015, 19:17:27 UTC | Updated version of gubbins package in install-userspace.sh | 20 April 2015, 19:17:27 UTC |
| 75e5a84 | andrewjpage | 16 April 2015, 15:10:13 UTC | Merge pull request #140 from andrewjpage/window_size_self_error Window size self error | 16 April 2015, 15:10:13 UTC |
| 374aa52 | andrewjpage | 16 April 2015, 15:09:40 UTC | max window size bug | 16 April 2015, 15:09:40 UTC |
| a1bb2b6 | andrewjpage | 16 April 2015, 15:08:24 UTC | max window size | 16 April 2015, 15:08:24 UTC |
| e8914d0 | andrewjpage | 16 April 2015, 15:02:09 UTC | Merge pull request #139 from andrewjpage/window_size_self_error Window size self error | 16 April 2015, 15:02:09 UTC |
| 0213034 | andrewjpage | 16 April 2015, 15:01:14 UTC | version 1.3.21 | 16 April 2015, 15:01:14 UTC |
| fdd2a32 | andrewjpage | 16 April 2015, 14:52:11 UTC | pass in self to Gubbins | 16 April 2015, 14:52:11 UTC |
| 5f9c17e | andrewjpage | 16 April 2015, 14:33:56 UTC | Merge pull request #138 from andrewjpage/recalculate_genome_length version 1.3.1 | 16 April 2015, 14:33:56 UTC |
| b5b73f6 | andrewjpage | 16 April 2015, 14:32:03 UTC | Merge pull request #137 from andrewjpage/recalculate_genome_length Recalculate genome length | 16 April 2015, 14:32:03 UTC |
| 4e83bb8 | andrewjpage | 16 April 2015, 14:11:37 UTC | version 1.3.1 | 16 April 2015, 14:11:37 UTC |
| ec5904e | andrewjpage | 16 April 2015, 14:09:25 UTC | output genome length minus gaps and recomb as separate stat | 16 April 2015, 14:09:25 UTC |
| 81368c3 | andrewjpage | 14 April 2015, 15:41:12 UTC | calculate genome length for branch as excluding parent recombinations | 14 April 2015, 15:41:12 UTC |
| d7f49b6 | andrewjpage | 14 April 2015, 13:17:24 UTC | Merge pull request #136 from andrewjpage/downstream_recombinations Downstream recombinations | 14 April 2015, 13:17:24 UTC |
| f905435 | andrewjpage | 14 April 2015, 13:14:26 UTC | check input values for window size | 14 April 2015, 13:14:26 UTC |
| 9914f1e | andrewjpage | 14 April 2015, 13:06:50 UTC | allow window size to be set in python | 14 April 2015, 13:06:50 UTC |
| 6eecfa3 | andrewjpage | 14 April 2015, 12:37:06 UTC | pass window max and min in | 14 April 2015, 12:37:06 UTC |
| 1cf5c80 | andrewjpage | 13 April 2015, 14:28:24 UTC | revert to per branch | 13 April 2015, 14:28:24 UTC |
| 16eafeb | andrewjpage | 13 April 2015, 14:05:07 UTC | number of blocks includes all parents | 13 April 2015, 14:05:07 UTC |
| 9967faf | andrewjpage | 13 April 2015, 13:41:22 UTC | update number of snps stats | 13 April 2015, 13:41:22 UTC |
| ed3551f | andrewjpage | 13 April 2015, 13:19:09 UTC | version 1.3.0 | 13 April 2015, 13:19:09 UTC |
| 2ad5336 | andrewjpage | 13 April 2015, 13:15:24 UTC | convert from coords to index in single block test | 13 April 2015, 13:15:24 UTC |
| dd0a537 | andrewjpage | 13 April 2015, 13:05:53 UTC | use merged coords | 13 April 2015, 13:05:53 UTC |
| 03b8935 | andrewjpage | 13 April 2015, 11:04:31 UTC | include the current nodes blocks | 13 April 2015, 11:04:31 UTC |
| 7b7c3af | andrewjpage | 13 April 2015, 10:32:18 UTC | make output array big enough to hold all snps | 13 April 2015, 10:32:18 UTC |
| a20b101 | andrewjpage | 13 April 2015, 10:26:48 UTC | pass through length of snp_locations array | 13 April 2015, 10:26:48 UTC |
| d460593 | andrewjpage | 09 April 2015, 11:11:02 UTC | extra test for a single block | 09 April 2015, 11:11:02 UTC |
| 9482d25 | andrewjpage | 07 April 2015, 10:19:48 UTC | order of indices depends on order of blocks | 07 April 2015, 10:19:48 UTC |
| b99bd75 | andrewjpage | 07 April 2015, 10:15:53 UTC | initialise snp index list | 07 April 2015, 10:15:53 UTC |
| 9ce983d | andrewjpage | 07 April 2015, 10:06:41 UTC | non overlapping block | 07 April 2015, 10:06:41 UTC |
| 0655286 | andrewjpage | 07 April 2015, 10:01:45 UTC | remove debugging | 07 April 2015, 10:01:45 UTC |
| c39864a | andrewjpage | 07 April 2015, 10:01:04 UTC | remove duplicate indices | 07 April 2015, 10:01:04 UTC |
| 0011076 | andrewjpage | 07 April 2015, 09:46:03 UTC | version 1.2.5 | 07 April 2015, 09:46:03 UTC |
| 93f4ec0 | andrewjpage | 07 April 2015, 09:45:03 UTC | block out snps in downstream recombinations | 07 April 2015, 09:45:03 UTC |
| 4d193d8 | andrewjpage | 31 March 2015, 14:02:24 UTC | Merge pull request #135 from andrewjpage/script_version_number output version in python script | 31 March 2015, 14:02:24 UTC |
| f41a877 | andrewjpage | 31 March 2015, 14:01:56 UTC | output version in python script | 31 March 2015, 14:01:56 UTC |
| bdd1854 | andrewjpage | 30 March 2015, 13:59:12 UTC | Merge branch 'master' of github.com:sanger-pathogens/gubbins | 30 March 2015, 13:59:12 UTC |
| 329306d | andrewjpage | 30 March 2015, 13:58:47 UTC | eggs werent included in deb | 30 March 2015, 13:58:47 UTC |
| 15dede9 | andrewjpage | 30 March 2015, 13:18:52 UTC | Merge pull request #134 from andrewjpage/master include last element of array | 30 March 2015, 13:18:52 UTC |
| 6ec565c | andrewjpage | 30 March 2015, 13:18:11 UTC | include last element of array | 30 March 2015, 13:18:11 UTC |
| 7b597ff | andrewjpage | 30 March 2015, 10:37:55 UTC | Merge pull request #133 from andrewjpage/correct_vcf_format Correct vcf format and EMBL format | 30 March 2015, 10:37:55 UTC |
| c10301f | andrewjpage | 30 March 2015, 10:36:52 UTC | update version | 30 March 2015, 10:36:52 UTC |
| 3b68a20 | andrewjpage | 30 March 2015, 10:35:06 UTC | add quotes to tab files test | 30 March 2015, 10:35:06 UTC |
