| f571b77 | Nick Croucher | 01 December 2023, 13:14:37 UTC | Enlarge logo | 01 December 2023, 13:14:37 UTC |
| 5815e22 | Nick Croucher | 01 December 2023, 13:13:46 UTC | Move logo | 01 December 2023, 13:13:46 UTC |
| dd1f86b | Nick Croucher | 01 December 2023, 13:12:35 UTC | Reformat images | 01 December 2023, 13:12:35 UTC |
| 9da40ca | Nick Croucher | 01 December 2023, 13:10:44 UTC | Change logo size | 01 December 2023, 13:10:44 UTC |
| 287620e | Nick Croucher | 01 December 2023, 13:09:09 UTC | Change logo size | 01 December 2023, 13:09:09 UTC |
| 193fc4a | Nick Croucher | 01 December 2023, 13:06:51 UTC | Change logo size | 01 December 2023, 13:06:51 UTC |
| 3ea3af7 | Nick Croucher | 01 December 2023, 13:05:16 UTC | Change logo size | 01 December 2023, 13:05:16 UTC |
| c7928ce | Nick Croucher | 01 December 2023, 13:03:41 UTC | Add a logo | 01 December 2023, 13:03:41 UTC |
| 390b9da | Nick Croucher | 01 December 2023, 13:02:40 UTC | Merge branch 'master' of https://github.com/nickjcroucher/gubbins | 01 December 2023, 13:02:40 UTC |
| d19e64a | Nick Croucher | 01 December 2023, 13:02:30 UTC | Add a logo | 01 December 2023, 13:02:30 UTC |
| 89a1e55 | nickjcroucher | 30 November 2023, 18:55:09 UTC | Merge pull request #389 from nickjcroucher/add_seed Enable seed specification | 30 November 2023, 18:55:09 UTC |
| b8dbdb4 | Nick Croucher | 30 November 2023, 14:58:31 UTC | Update installation instructions (#152) | 30 November 2023, 14:58:31 UTC |
| bf3bd21 | Nick Croucher | 30 November 2023, 13:42:40 UTC | Prioritise parallelised version of fasttree | 30 November 2023, 13:42:40 UTC |
| b4e7a92 | Nick Croucher | 30 November 2023, 13:23:10 UTC | Add missing example | 30 November 2023, 13:23:10 UTC |
| 9228a0d | Nick Croucher | 30 November 2023, 13:19:08 UTC | Describe development plans | 30 November 2023, 13:19:08 UTC |
| 52a6885 | Nick Croucher | 30 November 2023, 11:52:21 UTC | Enable seed specification | 30 November 2023, 11:52:21 UTC |
| 6d5f0af | Nick Croucher | 18 September 2023, 07:05:55 UTC | Fix formatting | 18 September 2023, 07:05:55 UTC |
| 62459a8 | Nick Croucher | 14 September 2023, 13:54:33 UTC | Fix URL using DOI | 14 September 2023, 13:54:33 UTC |
| bbde961 | Nick Croucher | 14 September 2023, 13:53:11 UTC | Change URL to use DOI | 14 September 2023, 13:53:11 UTC |
| 64ec926 | Nick Croucher | 13 September 2023, 04:59:32 UTC | Add bioconda patch | 13 September 2023, 04:59:32 UTC |
| aa14e1f | Nick Croucher | 11 September 2023, 07:29:27 UTC | Bump version | 11 September 2023, 07:29:27 UTC |
| 79da6f0 | nickjcroucher | 11 September 2023, 07:18:27 UTC | Merge pull request #384 from nickjcroucher/new_ska2 Add plotting and fix OSX installation bug | 11 September 2023, 07:18:27 UTC |
| 1b689a7 | Nick Croucher | 11 September 2023, 05:42:05 UTC | Fix broken link | 11 September 2023, 05:42:05 UTC |
| abf65c6 | Nick Croucher | 11 September 2023, 05:38:32 UTC | Add necessary plotting commands | 11 September 2023, 05:38:32 UTC |
| fc6ee52 | Nick Croucher | 11 September 2023, 05:38:18 UTC | Add plotting documentation | 11 September 2023, 05:38:18 UTC |
| 62958a0 | Nick Croucher | 10 September 2023, 05:41:49 UTC | Update with links to plotting advice | 10 September 2023, 05:41:49 UTC |
| 5492366 | Nick Croucher | 10 September 2023, 05:34:17 UTC | Fix type in commands | 10 September 2023, 05:34:17 UTC |
| 1ebe4e5 | Nick Croucher | 09 September 2023, 17:28:02 UTC | Add comprehensive plotting tests | 09 September 2023, 17:28:02 UTC |
| 72fbefa | Nick Croucher | 09 September 2023, 17:27:35 UTC | Ensure compatibility with different inputs | 09 September 2023, 17:27:35 UTC |
| 865cfb1 | Nick Croucher | 08 September 2023, 20:06:55 UTC | Annotate main function | 08 September 2023, 20:06:55 UTC |
| 35498c0 | Nick Croucher | 08 September 2023, 19:50:46 UTC | Add input validation | 08 September 2023, 19:50:46 UTC |
| 7de52b9 | Nick Croucher | 08 September 2023, 19:18:54 UTC | Add clade annotation to plotting test | 08 September 2023, 19:18:54 UTC |
| f3893f4 | Nick Croucher | 08 September 2023, 18:59:24 UTC | Enable direct annotation of the tree | 08 September 2023, 18:59:24 UTC |
| a0b3fb4 | Nick Croucher | 08 September 2023, 12:58:47 UTC | Enable taxon label size adjustment | 08 September 2023, 12:58:47 UTC |
| 1bf8b49 | Nick Croucher | 08 September 2023, 10:54:17 UTC | Remove sudo to prevent cache permissions problems | 08 September 2023, 10:54:17 UTC |
| 4146c8f | Nick Croucher | 08 September 2023, 10:43:29 UTC | Distribute libclang across clang versions | 08 September 2023, 10:43:29 UTC |
| f04a3b2 | Nick Croucher | 08 September 2023, 05:04:10 UTC | Remove coverage flag from OSX compilation | 08 September 2023, 05:04:10 UTC |
| 4b75805 | Nick Croucher | 08 September 2023, 04:23:29 UTC | Ensure latest llvm | 08 September 2023, 04:23:29 UTC |
| 59456ac | Nick Croucher | 08 September 2023, 04:21:36 UTC | Fix annotation | 08 September 2023, 04:21:36 UTC |
| 5470b83 | Nick Croucher | 07 September 2023, 20:34:19 UTC | Fix kmer length | 07 September 2023, 20:34:19 UTC |
| 5880fae | Nick Croucher | 07 September 2023, 18:04:32 UTC | Add sequences to test | 07 September 2023, 18:04:32 UTC |
| b1774f9 | Nick Croucher | 07 September 2023, 18:01:30 UTC | Define prototype for main | 07 September 2023, 18:01:30 UTC |
| 4f2b2d3 | Nick Croucher | 07 September 2023, 17:42:47 UTC | Add unique sequences for ska test | 07 September 2023, 17:42:47 UTC |
| e9eddf4 | Nick Croucher | 07 September 2023, 15:25:58 UTC | Remove obsolete deletion command | 07 September 2023, 15:25:58 UTC |
| 3af2159 | Nick Croucher | 07 September 2023, 15:20:11 UTC | Correct interpreter path | 07 September 2023, 15:20:11 UTC |
| a65ca7d | Nick Croucher | 07 September 2023, 13:51:41 UTC | Update from setup.py to pip | 07 September 2023, 13:52:07 UTC |
| f50cb93 | Nick Croucher | 07 September 2023, 13:05:53 UTC | Update obsolete macro | 07 September 2023, 13:05:53 UTC |
| 2f7b077 | Nick Croucher | 07 September 2023, 10:40:45 UTC | Remove jellyfish deletion command | 07 September 2023, 10:40:45 UTC |
| 406e18a | Nick Croucher | 07 September 2023, 10:37:36 UTC | Add plotting test | 07 September 2023, 10:37:36 UTC |
| 8f54050 | Nick Croucher | 07 September 2023, 09:57:13 UTC | Update R dependencies for plotting | 07 September 2023, 09:57:13 UTC |
| 9d3ab7b | Nick Croucher | 07 September 2023, 09:50:04 UTC | Add R plotting script | 07 September 2023, 09:50:04 UTC |
| 1da11b9 | Nick Croucher | 22 June 2023, 11:10:14 UTC | Mask repeats with ska2 | 22 June 2023, 11:10:14 UTC |
| 97f24cd | Nick Croucher | 15 June 2023, 15:45:15 UTC | Add iso8601 dependency | 15 June 2023, 15:45:15 UTC |
| 28dcac1 | Nick Croucher | 15 June 2023, 15:27:57 UTC | Update history of changes | 15 June 2023, 15:27:57 UTC |
| deb7981 | Nick Croucher | 15 June 2023, 15:25:47 UTC | Fix hyperlink | 15 June 2023, 15:25:47 UTC |
| a15c6b7 | Nick Croucher | 15 June 2023, 15:21:48 UTC | Upgrade to node.js 16 | 15 June 2023, 15:21:48 UTC |
| f208636 | Nick Croucher | 15 June 2023, 12:39:35 UTC | Add filtering of repeat sequences | 15 June 2023, 12:39:35 UTC |
| a26e302 | Nick Croucher | 15 June 2023, 12:39:06 UTC | Remove version constraint | 15 June 2023, 12:39:06 UTC |
| 336fd03 | Nick Croucher | 15 June 2023, 12:16:49 UTC | Add jellyfish for k-mer counting | 15 June 2023, 12:16:49 UTC |
| 21e70de | Nick Croucher | 05 May 2023, 07:14:44 UTC | Update to use SKA2 | 05 May 2023, 07:14:44 UTC |
| 2c3c7c2 | nickjcroucher | 05 May 2023, 07:12:01 UTC | Merge pull request #367 from nickjcroucher/alignment_updating Update alignment generation methods | 05 May 2023, 07:12:01 UTC |
| c2d0ac0 | Nick Croucher | 05 May 2023, 06:56:28 UTC | Update for new alignment generation | 05 May 2023, 06:56:28 UTC |
| e02866e | Nick Croucher | 05 May 2023, 06:41:47 UTC | Sort CSV headers | 05 May 2023, 06:41:47 UTC |
| 5434e03 | Nick Croucher | 05 May 2023, 06:16:29 UTC | Fix filename variable | 05 May 2023, 06:16:29 UTC |
| c7adbb7 | Nick Croucher | 05 May 2023, 06:07:10 UTC | Rearrange alignment summary output file | 05 May 2023, 06:07:10 UTC |
| d066650 | Nick Croucher | 05 May 2023, 05:37:05 UTC | Update versions for alignment generation | 05 May 2023, 05:37:05 UTC |
| a489caf | Nick Croucher | 05 May 2023, 05:32:59 UTC | Change k-mer length | 05 May 2023, 05:32:59 UTC |
| 12747bd | Nick Croucher | 05 May 2023, 05:11:55 UTC | Update alignment generation and formatting | 05 May 2023, 05:11:55 UTC |
| 1069d03 | Nick Croucher | 05 May 2023, 04:23:47 UTC | Update ska alignment testing script | 05 May 2023, 04:23:47 UTC |
| 31c80fe | Nick Croucher | 04 May 2023, 20:45:37 UTC | Upgrade to ska2 | 04 May 2023, 20:45:37 UTC |
| 6999fbf | Nick Croucher | 04 May 2023, 17:02:16 UTC | Add test for alignment reformatting | 04 May 2023, 17:02:16 UTC |
| 52ad7dd | Nick Croucher | 04 May 2023, 16:47:03 UTC | Enable reformatting of alignments | 04 May 2023, 16:47:03 UTC |
| 425fc43 | Nick Croucher | 04 May 2023, 16:16:13 UTC | Update command line parsing | 04 May 2023, 16:16:13 UTC |
| 5f01b03 | Nick Croucher | 04 May 2023, 16:08:00 UTC | Change alignment checker output file names | 04 May 2023, 16:08:00 UTC |
| f7ef47e | Nick Croucher | 21 April 2023, 07:57:01 UTC | Bump version | 21 April 2023, 07:57:01 UTC |
| 3cfec5c | Nick Croucher | 21 April 2023, 06:35:22 UTC | Pin numpy version for numba compatibility | 21 April 2023, 06:35:22 UTC |
| 6f9cd03 | nickjcroucher | 08 March 2023, 13:31:10 UTC | Merge pull request #363 from nickjcroucher/rec_per_gene Add script for quantifying recombination per gene | 08 March 2023, 13:31:10 UTC |
| 0b19f91 | Nick Croucher | 08 March 2023, 10:15:54 UTC | Fix python rec counting script command | 08 March 2023, 10:16:24 UTC |
| 60bc23f | Nick Croucher | 08 March 2023, 09:42:58 UTC | Fix variable name | 08 March 2023, 09:42:58 UTC |
| d9a073a | Nick Croucher | 08 March 2023, 09:32:56 UTC | Add recombination counting script | 08 March 2023, 09:32:56 UTC |
| e3e17bf | Nick Croucher | 08 March 2023, 09:32:18 UTC | Update recombination counting output | 08 March 2023, 09:32:18 UTC |
| 9144fb4 | Nick Croucher | 06 March 2023, 16:51:27 UTC | Add recombination enumeration script | 06 March 2023, 16:51:27 UTC |
| f5e87ed | Nick Croucher | 06 March 2023, 16:46:45 UTC | Add script for countig recombinations affecting genes | 06 March 2023, 16:46:45 UTC |
| 2c11f7e | Nick Croucher | 27 February 2023, 14:41:08 UTC | Fix error message printing | 27 February 2023, 14:41:08 UTC |
| ce9d64f | Nick Croucher | 06 October 2022, 09:50:11 UTC | Update to v3.3 | 06 October 2022, 09:50:11 UTC |
| b83a607 | nickjcroucher | 06 October 2022, 09:46:06 UTC | Merge pull request #350 from nickjcroucher/time_tree Merge in capacity to generate time-calibrated trees | 06 October 2022, 09:46:06 UTC |
| 079d890 | Nick Croucher | 06 October 2022, 09:10:49 UTC | Add correct reference files | 06 October 2022, 09:10:49 UTC |
| 6032bc3 | Nick Croucher | 06 October 2022, 08:59:00 UTC | Update script description | 06 October 2022, 08:59:00 UTC |
| ea1b51a | Nick Croucher | 06 October 2022, 08:56:51 UTC | Add files for generate script test | 06 October 2022, 08:56:51 UTC |
| 515d61d | Nick Croucher | 06 October 2022, 08:33:32 UTC | Rename script and install | 06 October 2022, 08:33:32 UTC |
| 60e9541 | Nick Croucher | 06 October 2022, 08:32:24 UTC | Enable generation of filtered clade | 06 October 2022, 08:32:24 UTC |
| 05f11d0 | Nick Croucher | 06 October 2022, 07:32:08 UTC | Update documentation | 06 October 2022, 07:32:08 UTC |
| 883a1c5 | Nick Croucher | 06 October 2022, 07:31:52 UTC | Log updates | 06 October 2022, 07:31:52 UTC |
| 3672bd4 | Nick Croucher | 06 October 2022, 07:31:39 UTC | Fix hybrid mode | 06 October 2022, 07:31:39 UTC |
| ac839ac | Nick Croucher | 06 October 2022, 05:32:26 UTC | Correct arguments in failing test | 06 October 2022, 05:32:26 UTC |
| f315d55 | Nick Croucher | 05 October 2022, 20:35:11 UTC | Enable processing of custom models | 05 October 2022, 20:35:11 UTC |
| 78e9e9b | Nick Croucher | 05 October 2022, 19:26:56 UTC | Use time calibration for sequence reconstruction | 05 October 2022, 19:26:56 UTC |
| 3d06e04 | Nick Croucher | 05 October 2022, 18:12:27 UTC | Create model test object | 05 October 2022, 18:12:27 UTC |
| fe286ed | Nick Croucher | 05 October 2022, 14:49:01 UTC | Correct default models | 05 October 2022, 14:49:01 UTC |
| 875a3b7 | Nick Croucher | 05 October 2022, 14:34:24 UTC | Change default model fitting algorithm | 05 October 2022, 14:34:24 UTC |
