| b7b935d | andrewjpage | 22 September 2017, 10:57:33 UTC | Merge branch 'internal_nodes' | 22 September 2017, 10:57:33 UTC |
| 5d8676e | andrewjpage | 22 September 2017, 10:56:03 UTC | Merge branch 'master' of github.com:sanger-pathogens/gubbins into internal_nodes | 22 September 2017, 10:56:03 UTC |
| abae76f | andrewjpage | 22 September 2017, 10:55:46 UTC | fix changelog | 22 September 2017, 10:55:46 UTC |
| 3a276c0 | andrewjpage | 22 September 2017, 10:54:52 UTC | Merge pull request #202 from andrewjpage/internal_nodes Internal nodes | 22 September 2017, 10:54:52 UTC |
| b03434a | andrewjpage | 22 September 2017, 10:53:57 UTC | test for internal labels | 22 September 2017, 10:53:57 UTC |
| 63134f3 | andrewjpage | 22 September 2017, 10:02:33 UTC | inc version | 22 September 2017, 10:02:33 UTC |
| e5c97f2 | andrewjpage | 22 September 2017, 10:01:17 UTC | add internal node labels to the final tree | 22 September 2017, 10:01:17 UTC |
| dbe0b71 | andrewjpage | 21 September 2017, 14:33:23 UTC | Merge pull request #201 from andrewjpage/gubbins_drawer_help Gubbins drawer help text | 21 September 2017, 14:33:23 UTC |
| c1305e7 | andrewjpage | 21 September 2017, 14:27:45 UTC | assume 1 file | 21 September 2017, 14:27:45 UTC |
| decfc5f | andrewjpage | 21 September 2017, 14:02:31 UTC | Add helptext to gubbins drawer and require tree as a positional argument rather than an option. | 21 September 2017, 14:02:31 UTC |
| 0e6774a | andrewjpage | 15 September 2017, 13:34:52 UTC | gubbins drawer to use argsparse | 15 September 2017, 13:34:52 UTC |
| 3ad41e8 | andrewjpage | 15 September 2017, 13:04:25 UTC | Merge pull request #200 from andrewjpage/helptext Fix default extended help text. | 15 September 2017, 13:04:25 UTC |
| 30b8cb0 | andrewjpage | 15 September 2017, 13:03:47 UTC | changelog version | 15 September 2017, 13:03:47 UTC |
| d983d0b | andrewjpage | 15 September 2017, 12:58:55 UTC | force defaults to always print | 15 September 2017, 12:58:55 UTC |
| f796262 | andrewjpage | 04 September 2017, 10:10:32 UTC | Update CHANGELOG | 04 September 2017, 10:10:32 UTC |
| 79501ae | andrewjpage | 04 September 2017, 10:09:27 UTC | Merge pull request #197 from andrewjpage/avx2 allow for AVX2 | 04 September 2017, 10:09:27 UTC |
| b907ad4 | andrewjpage | 04 September 2017, 10:05:21 UTC | allow for AVX2 | 04 September 2017, 10:05:21 UTC |
| 1d13185 | ssjunnebo | 02 August 2017, 12:10:44 UTC | Merge pull request #193 from ssjunnebo/master updated manual | 02 August 2017, 12:10:44 UTC |
| d8a2b9d | Sara Sjunnebo | 02 August 2017, 12:08:41 UTC | updated manual | 02 August 2017, 12:08:41 UTC |
| 8e6109c | andrewjpage | 21 June 2017, 15:39:59 UTC | Update README.md | 21 June 2017, 15:39:59 UTC |
| 933d50e | andrewjpage | 21 June 2017, 13:29:38 UTC | Update INSTALL.md | 21 June 2017, 13:29:38 UTC |
| b1a1186 | ssjunnebo | 13 March 2017, 14:02:36 UTC | Merge pull request #188 from ssjunnebo/master Manual in docx format | 13 March 2017, 14:02:36 UTC |
| 5a1ff3a | ssjunnebo | 13 March 2017, 13:57:06 UTC | Added latest manual in docx format | 13 March 2017, 13:57:06 UTC |
| 863d44f | ssjunnebo | 20 February 2017, 15:04:07 UTC | Merge pull request #186 from ssjunnebo/master Fixed biopython sub_features bug | 20 February 2017, 15:04:07 UTC |
| 6f3af4a | Sara Sjunnebo | 20 February 2017, 15:02:37 UTC | change version nr | 20 February 2017, 15:02:37 UTC |
| f0eb50f | Sara Sjunnebo | 20 February 2017, 14:51:21 UTC | Merge branch '516666' | 20 February 2017, 14:51:21 UTC |
| cef2dcc | Sara Sjunnebo | 20 February 2017, 14:49:57 UTC | gubbins_drawer.py fixed biopython error | 20 February 2017, 14:49:57 UTC |
| dbb278c | andrewjpage | 31 October 2016, 13:45:01 UTC | Update CHANGELOG | 31 October 2016, 13:45:01 UTC |
| 5bb1896 | andrewjpage | 31 October 2016, 13:12:07 UTC | Merge pull request #180 from andrewjpage/dont_filter_identical_sequences_by_default dont filter out identical sequences by default | 31 October 2016, 13:12:07 UTC |
| 3472753 | andrewjpage | 31 October 2016, 13:09:09 UTC | dont filter out identical sequences by default | 31 October 2016, 13:09:09 UTC |
| 8a12ae7 | andrewjpage | 01 August 2016, 15:05:52 UTC | Merge branch 'master' of github.com:sanger-pathogens/gubbins | 01 August 2016, 15:05:52 UTC |
| c2eb532 | andrewjpage | 01 August 2016, 15:05:27 UTC | Dockerfile | 01 August 2016, 15:05:27 UTC |
| 28b83fc | andrewjpage | 25 July 2016, 12:43:03 UTC | Update README.md | 25 July 2016, 12:43:03 UTC |
| 599c7e1 | andrewjpage | 22 July 2016, 13:58:50 UTC | Update README.md | 22 July 2016, 13:58:50 UTC |
| ff12945 | andrewjpage | 22 July 2016, 13:57:43 UTC | Update README.md | 22 July 2016, 13:57:43 UTC |
| cd83da2 | andrewjpage | 22 July 2016, 13:57:23 UTC | Update README.md | 22 July 2016, 13:57:23 UTC |
| 99d6756 | andrewjpage | 22 July 2016, 13:32:22 UTC | Merge pull request #175 from andrewjpage/speedup Use GTRCAT by default with RAxML | 22 July 2016, 13:32:22 UTC |
| 18cbead | andrewjpage | 22 July 2016, 13:23:18 UTC | raxml 7.8 doesnt like missing blank line at end of test fasta | 22 July 2016, 13:23:18 UTC |
| 8ac5ceb | andrewjpage | 22 July 2016, 13:11:48 UTC | GTRCAT by default in RAxML | 22 July 2016, 13:11:48 UTC |
| 3487292 | andrewjpage | 22 July 2016, 10:57:50 UTC | remove unnessisary loops when finding recombination bases | 22 July 2016, 10:57:50 UTC |
| b868e40 | andrewjpage | 22 July 2016, 09:49:10 UTC | Update INSTALL.md | 22 July 2016, 09:49:10 UTC |
| a5f4fc0 | andrewjpage | 15 July 2016, 17:13:08 UTC | Merge pull request #172 from andrewjpage/raxml_reconstruction Raxml reconstruction | 15 July 2016, 17:13:08 UTC |
| 39e8852 | andrewjpage | 14 July 2016, 09:59:13 UTC | change permissions on test | 14 July 2016, 09:59:13 UTC |
| ce5bc10 | andrewjpage | 14 July 2016, 09:27:25 UTC | use teardown for tests, rename internal node prefix | 14 July 2016, 09:27:25 UTC |
| 07175a3 | andrewjpage | 13 July 2016, 10:47:19 UTC | print internal tree command in verbose mode | 13 July 2016, 10:47:19 UTC |
| bbd7720 | andrewjpage | 12 July 2016, 14:58:50 UTC | tests pass | 12 July 2016, 14:58:50 UTC |
| 4c117f4 | andrewjpage | 11 July 2016, 15:42:44 UTC | wip | 12 July 2016, 14:44:58 UTC |
| fc1c04e | andrewjpage | 27 May 2016, 10:28:06 UTC | base sequence reconstruction | 06 July 2016, 13:10:51 UTC |
| 5404925 | andrewjpage | 21 April 2016, 13:33:55 UTC | ubuntu 16.04 | 21 April 2016, 13:33:55 UTC |
| a4b6c1d | andrewjpage | 15 April 2016, 12:27:52 UTC | Merge pull request #166 from andrewjpage/duplicate_sequences Duplicate sequences | 15 April 2016, 12:27:52 UTC |
| 5f48483 | andrewjpage | 14 April 2016, 15:26:46 UTC | fix tests which werent running remove duplicates and missing data move some fasta validation to new file changelog description of change update versions for travis rename fasttree arch make variables rename fastml dir add v before version number | 15 April 2016, 12:26:54 UTC |
| d0ea1bb | andrewjpage | 14 April 2016, 10:37:32 UTC | hash input sequences | 14 April 2016, 10:37:32 UTC |
| 677be48 | andrewjpage | 13 April 2016, 09:59:20 UTC | update version number | 13 April 2016, 09:59:20 UTC |
| ee61719 | andrewjpage | 13 April 2016, 09:55:06 UTC | Merge branch 'master' of github.com:sanger-pathogens/gubbins | 13 April 2016, 09:55:06 UTC |
| 88c91d2 | andrewjpage | 12 April 2016, 17:58:19 UTC | Merge pull request #164 from harvardinformatics/master Convert the proc output from bytes to strings | 12 April 2016, 17:58:19 UTC |
| 74de8b9 | Aaron Kitzmiller | 12 April 2016, 14:49:25 UTC | Convert the proc output from bytes to strings so that comparisons will work. | 12 April 2016, 14:49:25 UTC |
| d9dfff8 | andrewjpage | 09 March 2016, 10:28:32 UTC | remove homebrew directory | 09 March 2016, 10:28:32 UTC |
| fe094b0 | andrewjpage | 01 March 2016, 09:49:02 UTC | Merge branch 'master' of github.com:sanger-pathogens/gubbins | 01 March 2016, 09:49:02 UTC |
| baa595b | andrewjpage | 01 March 2016, 09:48:42 UTC | more informative changelog | 01 March 2016, 09:48:42 UTC |
| 3f9e92c | andrewjpage | 01 March 2016, 09:06:07 UTC | Update README.md | 01 March 2016, 09:06:07 UTC |
| ce39645 | andrewjpage | 01 March 2016, 09:01:03 UTC | midpoint rerooting | 01 March 2016, 09:01:03 UTC |
| e2adff3 | andrewjpage | 29 February 2016, 16:16:22 UTC | update version | 29 February 2016, 16:16:22 UTC |
| 1b4b312 | andrewjpage | 29 February 2016, 16:15:14 UTC | Merge pull request #161 from jeromekelleher/fix-stack-allocation2 Fix allocation from stack bug. | 29 February 2016, 16:15:14 UTC |
| 49db81e | andrewjpage | 29 February 2016, 16:15:02 UTC | Merge pull request #163 from andrewjpage/master midpoint rerooting by default | 29 February 2016, 16:15:02 UTC |
| bcc3b87 | andrewjpage | 29 February 2016, 15:19:27 UTC | update version | 29 February 2016, 15:19:27 UTC |
| 5a29de8 | andrewjpage | 29 February 2016, 15:18:48 UTC | midpoint rerooting by default | 29 February 2016, 15:18:48 UTC |
| 3960753 | Jerome Kelleher | 19 February 2016, 23:00:15 UTC | Fix allocation from stack bug. For large numbers of SNPs allocating from the stack caused a segfault. This fixes the issue by allocating from the heap with malloc. | 19 February 2016, 23:00:15 UTC |
| c5c8dec | andrewjpage | 13 January 2016, 11:31:14 UTC | Merge pull request #160 from andrewjpage/remove_install_sh remove install-sh | 13 January 2016, 11:31:14 UTC |
| 24cb554 | andrewjpage | 13 January 2016, 11:24:29 UTC | remove install-sh | 13 January 2016, 11:24:29 UTC |
| 003b908 | andrewjpage | 11 December 2015, 09:21:16 UTC | Update INSTALL.md | 11 December 2015, 09:21:16 UTC |
| 635aaac | andrewjpage | 09 December 2015, 15:52:28 UTC | Merge pull request #158 from andrewjpage/debian_bug_807150 Debian bug 807150 | 09 December 2015, 15:52:28 UTC |
| 336f824 | andrewjpage | 09 December 2015, 15:43:56 UTC | linux only library | 09 December 2015, 15:43:56 UTC |
| 29936b9 | andrewjpage | 09 December 2015, 15:42:40 UTC | Allow space for EOF | 09 December 2015, 15:42:40 UTC |
| 0e3b263 | andrewjpage | 19 November 2015, 10:02:23 UTC | update version | 19 November 2015, 10:02:23 UTC |
| 2fef7c1 | andrewjpage | 19 November 2015, 10:01:41 UTC | keep change log | 19 November 2015, 10:01:41 UTC |
| b74392e | andrewjpage | 19 November 2015, 10:01:20 UTC | remove debian directory | 19 November 2015, 10:01:20 UTC |
| a81dbbe | andrewjpage | 02 September 2015, 15:07:47 UTC | Merge pull request #153 from andrewjpage/filename_length check for input files which are too long | 02 September 2015, 15:07:47 UTC |
| eeb4408 | andrewjpage | 02 September 2015, 13:48:14 UTC | check for input files which are too long | 02 September 2015, 13:48:14 UTC |
| 869c665 | andrewjpage | 16 July 2015, 08:33:51 UTC | official brew | 16 July 2015, 08:33:51 UTC |
| 091cecf | andrewjpage | 08 July 2015, 13:03:02 UTC | update install instructions | 08 July 2015, 13:03:02 UTC |
| 055d444 | andrewjpage | 07 July 2015, 14:40:58 UTC | Merge pull request #150 from andrewjpage/master update install docs | 07 July 2015, 14:40:58 UTC |
| 0d0bb60 | andrewjpage | 07 July 2015, 14:39:54 UTC | update version | 07 July 2015, 14:39:54 UTC |
| 5d06468 | andrewjpage | 07 July 2015, 14:39:35 UTC | update installation instructions and python setup dependancy names | 07 July 2015, 14:39:35 UTC |
| 9851b27 | andrewjpage | 04 July 2015, 08:35:11 UTC | update install to use pip3 | 04 July 2015, 08:35:11 UTC |
| db80ecc | andrewjpage | 01 July 2015, 15:47:57 UTC | fix formatting | 01 July 2015, 15:47:57 UTC |
| 21757dc | andrewjpage | 01 July 2015, 15:41:09 UTC | Merge pull request #149 from andrewjpage/convert_python_to_3 Convert python to 3 | 01 July 2015, 15:41:09 UTC |
| 7d41f9b | andrewjpage | 01 July 2015, 15:32:19 UTC | new installation instructions | 01 July 2015, 15:32:19 UTC |
| b1db052 | andrewjpage | 01 July 2015, 15:17:50 UTC | homebrew/linuxbrew instructions | 01 July 2015, 15:17:50 UTC |
| d75e48e | andrewjpage | 01 July 2015, 10:26:07 UTC | return statments in test helper | 01 July 2015, 10:26:07 UTC |
| c4363b4 | andrewjpage | 01 July 2015, 09:40:28 UTC | force end character for clang | 01 July 2015, 09:40:28 UTC |
| 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 |
