| 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 |
| acc2e48 | Nick Croucher | 05 October 2022, 11:45:42 UTC | Fix typo | 05 October 2022, 11:45:42 UTC |
| e70f0c9 | Nick Croucher | 05 October 2022, 11:22:05 UTC | Fix star phylogeny information | 05 October 2022, 11:22:05 UTC |
| a71519b | Nick Croucher | 05 October 2022, 11:06:21 UTC | Greater model selection flexibility | 05 October 2022, 11:06:21 UTC |
| 71d1d16 | Nick Croucher | 05 October 2022, 09:51:41 UTC | Increase logging detail | 05 October 2022, 09:51:41 UTC |
| 3752f3e | Nick Croucher | 05 October 2022, 08:36:53 UTC | Add test for combination of methods | 05 October 2022, 08:36:53 UTC |
| 3502174 | Nick Croucher | 05 October 2022, 08:26:26 UTC | Fix reconstruction selection | 05 October 2022, 08:26:26 UTC |
| 50ba440 | Nick Croucher | 05 October 2022, 05:34:42 UTC | Add iqtree-fast tests | 05 October 2022, 05:34:42 UTC |
| cccc15b | Nick Croucher | 05 October 2022, 05:28:14 UTC | Remove hard coded variable | 05 October 2022, 05:28:14 UTC |
| 185827d | Nick Croucher | 05 October 2022, 05:25:40 UTC | Maintain branch scale with LSD | 05 October 2022, 05:25:40 UTC |
| c1224be | Nick Croucher | 04 October 2022, 15:14:58 UTC | Simplify model functions | 04 October 2022, 15:14:58 UTC |
| 0b83712 | Nick Croucher | 04 October 2022, 14:51:40 UTC | Improve phylogenetic model processing | 04 October 2022, 14:51:40 UTC |
| 894c5e7 | Nick Croucher | 03 October 2022, 08:15:56 UTC | Fix date filename | 03 October 2022, 08:15:56 UTC |
| 18f4051 | Nick Croucher | 03 October 2022, 07:36:14 UTC | Enable generation of time-calibrated trees | 03 October 2022, 07:36:14 UTC |
| 3eb87c8 | Nick Croucher | 29 September 2022, 08:24:13 UTC | Update iqtree version | 29 September 2022, 08:24:13 UTC |
| 746b428 | Nick Croucher | 23 September 2022, 08:55:22 UTC | Add tests for new iqtree features and outgroups | 23 September 2022, 08:55:22 UTC |
| 4581de1 | Nick Croucher | 16 August 2022, 07:58:19 UTC | Change resume criterion | 16 August 2022, 07:58:19 UTC |
| ab18e3d | nickjcroucher | 19 July 2022, 18:16:48 UTC | Merge pull request #342 from nickjcroucher/issue_325 Fixes for #325 and #339 | 19 July 2022, 18:16:48 UTC |
| bec45e7 | Nick Croucher | 19 July 2022, 15:36:58 UTC | Fix filename error (#339) | 19 July 2022, 15:36:58 UTC |
| 6cf3cf1 | Nick Croucher | 19 July 2022, 15:34:44 UTC | Make algorithm name available and fix recon issue | 19 July 2022, 15:34:44 UTC |
| e9dcb7c | Nick Croucher | 16 July 2022, 05:03:49 UTC | Add test for mar in pairwise mode | 16 July 2022, 05:03:49 UTC |
| 0b2b0df | Nick Croucher | 15 July 2022, 16:21:37 UTC | Prevent mar in pairwise mode | 15 July 2022, 16:21:37 UTC |
| 96efe47 | Nick Croucher | 15 July 2022, 16:09:43 UTC | Clarify variable names | 15 July 2022, 16:09:43 UTC |
| c925d44 | nickjcroucher | 14 July 2022, 10:20:14 UTC | Merge pull request #341 from nickjcroucher/update_rec Add validation of datasets being combined | 14 July 2022, 10:20:14 UTC |
| 4d296db | Nick Croucher | 14 July 2022, 09:58:06 UTC | Add validation of datasets being combined | 14 July 2022, 09:58:06 UTC |
| eb7b75e | nickjcroucher | 24 May 2022, 10:00:59 UTC | Merge pull request #338 from nickjcroucher/update_rec v3.2.1 | 24 May 2022, 10:00:59 UTC |
| 5f80ed7 | Nick Croucher | 24 May 2022, 09:51:01 UTC | Update for v3.2.1 | 24 May 2022, 09:51:01 UTC |
| 921856d | Nick Croucher | 24 May 2022, 09:46:10 UTC | Update manual with resume option | 24 May 2022, 09:46:10 UTC |
| 068d3c2 | Nick Croucher | 24 May 2022, 09:16:39 UTC | Update extracted clade alignment | 24 May 2022, 09:16:39 UTC |
| be7efe3 | Nick Croucher | 24 May 2022, 08:56:48 UTC | Update mutable seq processing | 24 May 2022, 08:56:48 UTC |
| 3cfc160 | Nick Croucher | 24 May 2022, 08:50:01 UTC | Update tree extraction | 24 May 2022, 08:50:01 UTC |
| 8c4d190 | Nick Croucher | 24 May 2022, 08:49:09 UTC | Update clade extraction test files | 24 May 2022, 08:49:09 UTC |
| c7fc555 | Nick Croucher | 24 May 2022, 08:27:20 UTC | Add model specification | 24 May 2022, 08:27:20 UTC |
| a05405a | Nick Croucher | 24 May 2022, 08:19:11 UTC | Update clade extraction test output | 24 May 2022, 08:19:11 UTC |
| ba08a1e | Nick Croucher | 24 May 2022, 08:00:46 UTC | Add resumption tests | 24 May 2022, 08:00:46 UTC |
| 49c4429 | Nick Croucher | 24 May 2022, 05:20:02 UTC | Enable resumption of stalled runs | 24 May 2022, 05:20:02 UTC |
| 892b663 | Nick Croucher | 23 May 2022, 10:35:54 UTC | Update test files | 23 May 2022, 10:35:54 UTC |
| e023ee7 | Nick Croucher | 23 May 2022, 10:00:27 UTC | Formatting adjustments | 23 May 2022, 10:00:27 UTC |
| 12e6cbc | Nick Croucher | 18 May 2022, 07:41:48 UTC | Enable writing to file | 18 May 2022, 07:41:48 UTC |
| 9f409dd | Nick Croucher | 18 May 2022, 05:37:45 UTC | Make tree outputs consistent | 18 May 2022, 05:37:45 UTC |
| 39b8ea9 | Nick Croucher | 03 May 2022, 11:58:36 UTC | Formatting change | 03 May 2022, 11:58:36 UTC |
| 68afff3 | Nick Croucher | 03 May 2022, 11:25:11 UTC | Update manual with new options and outputs | 03 May 2022, 11:25:11 UTC |
| a1699c4 | Nick Croucher | 03 May 2022, 11:11:30 UTC | Update column heading | 03 May 2022, 11:11:30 UTC |
| 5927bce | Nick Croucher | 03 May 2022, 11:09:10 UTC | Improve output of analysis statistics | 03 May 2022, 11:09:10 UTC |
| b1f63c9 | Nick Croucher | 03 May 2022, 07:37:51 UTC | Correct array size value | 03 May 2022, 07:37:51 UTC |
| ec6f712 | Nick Croucher | 03 May 2022, 05:22:12 UTC | Fix verbose timing messages | 03 May 2022, 05:22:12 UTC |
| d2a39b9 | Nick Croucher | 02 May 2022, 20:42:03 UTC | Modify boundary conditions | 02 May 2022, 20:42:03 UTC |
| 74e2061 | Nick Croucher | 02 May 2022, 20:29:47 UTC | Update rerooting file naming | 02 May 2022, 20:29:47 UTC |
| 568fd07 | Nick Croucher | 02 May 2022, 20:21:52 UTC | Update rerooted trees | 02 May 2022, 20:21:52 UTC |
| f1e6ebc | Nick Croucher | 02 May 2022, 19:38:13 UTC | Update tree files | 02 May 2022, 19:38:13 UTC |
| a1f6871 | Nick Croucher | 02 May 2022, 18:49:47 UTC | Update expected tree | 02 May 2022, 18:49:47 UTC |
| e171618 | Nick Croucher | 02 May 2022, 18:40:40 UTC | Update expected recombination count | 02 May 2022, 18:40:40 UTC |
| ee35d62 | Nick Croucher | 02 May 2022, 18:40:13 UTC | Update test comparison file | 02 May 2022, 18:40:13 UTC |
| 1112270 | Nick Croucher | 02 May 2022, 13:09:33 UTC | Update snp counts | 02 May 2022, 13:09:33 UTC |
| 455a2ef | Nick Croucher | 02 May 2022, 12:57:16 UTC | Update window end unit tests | 02 May 2022, 12:57:16 UTC |
| d72ea1a | Nick Croucher | 02 May 2022, 05:33:08 UTC | Add CI message | 02 May 2022, 05:33:08 UTC |
| becc66e | Nick Croucher | 01 May 2022, 06:15:28 UTC | Merge updates Merge branch 'update_rec' of https://github.com/nickjcroucher/gubbins into update_rec | 01 May 2022, 06:15:28 UTC |
| 10d9351 | Nick Croucher | 01 May 2022, 06:14:57 UTC | Correct inequality | 01 May 2022, 06:14:57 UTC |
| 6752347 | jdaeth274 | 29 April 2022, 11:55:50 UTC | merging more informative verbose | 29 April 2022, 11:55:50 UTC |
| a531c9a | jdaeth274 | 29 April 2022, 11:53:39 UTC | tweaking the verbose output | 29 April 2022, 11:53:39 UTC |
| 1102ae1 | Nick Croucher | 29 April 2022, 11:46:47 UTC | Avoid multiprocessing with one thread | 29 April 2022, 11:46:47 UTC |
| 305b208 | Nick Croucher | 29 April 2022, 08:01:42 UTC | Parallelise over sites independently | 29 April 2022, 08:01:42 UTC |
| d7fd18d | Nick Croucher | 25 April 2022, 16:05:10 UTC | Correct variable name for file checking | 25 April 2022, 16:05:10 UTC |
| 4b10cef | Nick Croucher | 21 April 2022, 15:50:06 UTC | Avoid unnecessary recombination searching | 21 April 2022, 15:50:06 UTC |
| 67047df | Nick Croucher | 21 April 2022, 13:54:23 UTC | Iteratively reduce window size in recombination search | 21 April 2022, 13:54:23 UTC |
| 4a15f70 | Nick Croucher | 14 April 2022, 10:24:08 UTC | Improve rerooting with outgroup | 14 April 2022, 10:24:08 UTC |
| eb34da7 | Nick Croucher | 13 April 2022, 21:25:33 UTC | Add flag for extensive search | 13 April 2022, 21:25:33 UTC |
| 5efcb38 | Nick Croucher | 13 April 2022, 21:09:23 UTC | Restore correct copy syntax | 13 April 2022, 21:09:23 UTC |
| 561fad2 | Nick Croucher | 13 April 2022, 21:04:32 UTC | Update multiple recombinations check | 13 April 2022, 21:04:32 UTC |
| b88c0ee | Nick Croucher | 13 April 2022, 15:28:32 UTC | Update trees for tests | 13 April 2022, 15:28:32 UTC |
| 8678024 | Nick Croucher | 13 April 2022, 15:21:18 UTC | Update recombination counting function | 13 April 2022, 15:21:18 UTC |
| 50330c6 | Nick Croucher | 13 April 2022, 15:20:10 UTC | Update test command | 13 April 2022, 15:20:10 UTC |
| 0f9f7e1 | Nick Croucher | 13 April 2022, 15:15:34 UTC | Update multiple recombination expected files | 13 April 2022, 15:15:34 UTC |
| 49c32be | Nick Croucher | 13 April 2022, 15:14:54 UTC | Update multiple recombination expected files | 13 April 2022, 15:14:54 UTC |
| c054532 | Nick Croucher | 13 April 2022, 13:59:24 UTC | Change taxon order in tab file | 13 April 2022, 13:59:24 UTC |
| 7acf3db | Nick Croucher | 13 April 2022, 13:48:05 UTC | Add internal nodes to tree | 13 April 2022, 13:48:05 UTC |
| d795b25 | Nick Croucher | 13 April 2022, 13:37:07 UTC | Include node names in trees | 13 April 2022, 13:37:07 UTC |
| fbe31f1 | Nick Croucher | 13 April 2022, 12:37:40 UTC | Update JAR alignment for test | 13 April 2022, 12:37:40 UTC |
| 9e9387d | Nick Croucher | 13 April 2022, 12:26:45 UTC | Update tree for test | 13 April 2022, 12:26:45 UTC |
| 7f3d2a6 | Nick Croucher | 13 April 2022, 12:19:51 UTC | Updated expected result | 13 April 2022, 12:19:51 UTC |
| 2c14e59 | Nick Croucher | 13 April 2022, 11:03:46 UTC | Update multiple recombinations check | 13 April 2022, 11:03:46 UTC |
| ac4fb33 | Nick Croucher | 13 April 2022, 10:31:41 UTC | Update cutoff calculation | 13 April 2022, 10:31:41 UTC |
| e8fbb8c | Nick Croucher | 12 April 2022, 19:52:55 UTC | Fix recombinations at end of genome | 12 April 2022, 19:53:50 UTC |
| a97d3a7 | Nick Croucher | 12 April 2022, 10:42:09 UTC | Reformat function | 12 April 2022, 10:42:09 UTC |
| da4f26f | Nick Croucher | 08 April 2022, 09:11:04 UTC | Update run_gubbins calls | 08 April 2022, 09:11:04 UTC |
| 4503076 | Nick Croucher | 08 April 2022, 09:02:24 UTC | Add extensive search mode | 08 April 2022, 09:02:24 UTC |
| 826a282 | Nick Croucher | 08 April 2022, 08:18:24 UTC | Update threshold calculation | 08 April 2022, 08:18:24 UTC |
