| a051f2e | nickjcroucher | 12 October 2021, 06:19:10 UTC | Merge pull request #310 from sanger-pathogens/raxmlng_fix Fix to RAxML-NG | 12 October 2021, 06:19:10 UTC |
| 6c53184 | Nick Croucher | 12 October 2021, 06:18:02 UTC | Bump version | 12 October 2021, 06:18:02 UTC |
| efbd629 | Nick Croucher | 12 October 2021, 05:56:50 UTC | Add algorithmm detail | 12 October 2021, 05:56:50 UTC |
| 085e235 | Nick Croucher | 12 October 2021, 05:16:16 UTC | Use default starting trees for raxml-ng | 12 October 2021, 05:16:16 UTC |
| cf486da | Nick Croucher | 12 October 2021, 05:12:39 UTC | Use multiple starting trees for raxml-ng | 12 October 2021, 05:12:39 UTC |
| 9ba306a | Nick Croucher | 12 October 2021, 05:02:52 UTC | Fix software description | 12 October 2021, 05:02:52 UTC |
| 3053d4c | Nick Croucher | 11 October 2021, 20:37:26 UTC | Fix flag format | 11 October 2021, 20:37:26 UTC |
| 9b0e139 | Nick Croucher | 11 October 2021, 20:37:09 UTC | Fix typo | 11 October 2021, 20:37:09 UTC |
| ec2c6a5 | nickjcroucher | 11 October 2021, 15:07:43 UTC | Merge pull request #309 from sanger-pathogens/readme_correction Fix to manual | 11 October 2021, 15:07:43 UTC |
| f3d4c47 | Nick Croucher | 11 October 2021, 15:06:43 UTC | Fix to manual | 11 October 2021, 15:06:43 UTC |
| d9c0158 | nickjcroucher | 11 October 2021, 14:43:39 UTC | Merge pull request #308 from sanger-pathogens/more_docs Minor formatting changes to README | 11 October 2021, 14:43:39 UTC |
| 7e24faf | Nick Croucher | 11 October 2021, 14:42:36 UTC | Minor formatting changes | 11 October 2021, 14:42:36 UTC |
| 9ccf21f | nickjcroucher | 11 October 2021, 12:43:57 UTC | Merge pull request #307 from sanger-pathogens/docs_add Add statistical interpretation section to documentation | 11 October 2021, 12:43:57 UTC |
| b208840 | Nick Croucher | 11 October 2021, 12:42:35 UTC | Leave FTP hyperlinks | 11 October 2021, 12:42:35 UTC |
| 7544a2b | Nick Croucher | 11 October 2021, 12:41:44 UTC | Fix data hyperlinks | 11 October 2021, 12:41:44 UTC |
| 40e2976 | Nick Croucher | 11 October 2021, 12:39:37 UTC | Fix data hyperlinks | 11 October 2021, 12:39:37 UTC |
| 10c272e | Nick Croucher | 11 October 2021, 12:39:02 UTC | Fix data hyperlinks | 11 October 2021, 12:39:02 UTC |
| 4b1ba67 | Nick Croucher | 11 October 2021, 12:38:42 UTC | Fix data hyperlinks | 11 October 2021, 12:38:42 UTC |
| f113ab6 | Nick Croucher | 11 October 2021, 12:36:48 UTC | Add section on statistical interpretation | 11 October 2021, 12:36:48 UTC |
| b928290 | nickjcroucher | 11 October 2021, 10:51:58 UTC | Merge pull request #306 from sanger-pathogens/docs_update Update documentation | 11 October 2021, 10:51:58 UTC |
| 30a4d15 | Nick Croucher | 11 October 2021, 10:28:48 UTC | Highlight manual | 11 October 2021, 10:28:48 UTC |
| 0a0434b | Nick Croucher | 11 October 2021, 10:28:23 UTC | Highlight manual | 11 October 2021, 10:28:23 UTC |
| f9b641e | Nick Croucher | 11 October 2021, 10:27:09 UTC | Remove superfluous manual files | 11 October 2021, 10:27:09 UTC |
| 3319a5c | Nick Croucher | 11 October 2021, 10:26:22 UTC | Update image links | 11 October 2021, 10:26:22 UTC |
| b6e5308 | Nick Croucher | 11 October 2021, 10:23:08 UTC | Update image links | 11 October 2021, 10:23:08 UTC |
| 377edc0 | Nick Croucher | 11 October 2021, 10:21:03 UTC | Update image links | 11 October 2021, 10:21:03 UTC |
| 5c558eb | Nick Croucher | 11 October 2021, 10:18:04 UTC | Update doc linking | 11 October 2021, 10:18:04 UTC |
| f866e8c | Nick Croucher | 11 October 2021, 10:09:30 UTC | Update analysis examples | 11 October 2021, 10:09:30 UTC |
| 0437bfd | Nick Croucher | 11 October 2021, 09:41:23 UTC | Edits to relative link | 11 October 2021, 09:41:23 UTC |
| 3d3ef9c | Nick Croucher | 11 October 2021, 09:33:34 UTC | Update README for v3 | 11 October 2021, 09:33:34 UTC |
| cd190f8 | Nick Croucher | 11 October 2021, 09:21:15 UTC | Update documentation | 11 October 2021, 09:21:15 UTC |
| 3db99f5 | nickjcroucher | 06 October 2021, 21:13:00 UTC | Merge pull request #305 from sanger-pathogens/masking_aln Version 3.1 | 06 October 2021, 21:13:00 UTC |
| b85e832 | Nick Croucher | 06 October 2021, 20:51:16 UTC | Bump version | 06 October 2021, 20:51:16 UTC |
| 9aef629 | Nick Croucher | 06 October 2021, 20:42:26 UTC | Update FASTA input processing | 06 October 2021, 20:42:26 UTC |
| a093c2e | nickjcroucher | 06 October 2021, 19:52:06 UTC | Merge pull request #303 from jdaeth274/hpc_fix Removing hash and allowing for IUPAC codes | 06 October 2021, 19:52:06 UTC |
| 3a7179c | jdaeth274 | 06 October 2021, 12:58:22 UTC | Tidying error messages and removing debug statements | 06 October 2021, 12:58:22 UTC |
| dec08b0 | jdaeth274 | 06 October 2021, 10:50:49 UTC | remove dirs build and dist | 06 October 2021, 10:50:49 UTC |
| 5629d81 | jdaeth274 | 06 October 2021, 10:45:07 UTC | removing build and dist directories from python directory | 06 October 2021, 10:45:07 UTC |
| 8e540e2 | Nick Croucher | 06 October 2021, 09:19:02 UTC | Add tree topology checks | 06 October 2021, 09:19:02 UTC |
| df761b3 | Nick Croucher | 06 October 2021, 09:19:02 UTC | Add tree topology checks | 06 October 2021, 09:19:02 UTC |
| 234c745 | Nick Croucher | 05 October 2021, 12:48:17 UTC | Fix reconstruction inconsistency | 05 October 2021, 12:48:17 UTC |
| ec6325f | Nick Croucher | 05 October 2021, 12:48:17 UTC | Fix reconstruction inconsistency | 05 October 2021, 12:48:17 UTC |
| 57b3056 | jdaeth274 | 04 October 2021, 09:46:14 UTC | Merge branch 'masking_aln' of https://github.com/sanger-pathogens/gubbins into hpc_fix | 04 October 2021, 09:46:14 UTC |
| 6522664 | nickjcroucher | 30 September 2021, 20:40:50 UTC | Merge pull request #301 from sanger-pathogens/hpc_fix Hpc fix | 30 September 2021, 20:40:50 UTC |
| 8bf737f | nickjcroucher | 30 September 2021, 20:40:50 UTC | Merge pull request #301 from sanger-pathogens/hpc_fix Hpc fix | 30 September 2021, 20:40:50 UTC |
| 0d7487d | Nick Croucher | 30 September 2021, 20:36:58 UTC | Fix JAR method | 30 September 2021, 20:36:58 UTC |
| 31e07a1 | Nick Croucher | 30 September 2021, 20:36:58 UTC | Fix JAR method | 30 September 2021, 20:36:58 UTC |
| 6734d58 | jdaeth274 | 17 August 2021, 13:57:28 UTC | allowing for full run through | 17 August 2021, 13:57:28 UTC |
| 0cbd6de | jdaeth274 | 16 August 2021, 15:39:19 UTC | updating raxml-ng for full IUPAC codes | 16 August 2021, 15:39:19 UTC |
| cd0ff8e | jdaeth274 | 16 August 2021, 09:16:11 UTC | testing out the raxmlng recon | 16 August 2021, 09:16:11 UTC |
| 796872f | jdaeth274 | 13 August 2021, 16:38:39 UTC | checking intermediate file names | 13 August 2021, 16:38:39 UTC |
| 7b0b703 | jdaeth274 | 13 August 2021, 16:22:50 UTC | checking intermediate file names | 13 August 2021, 16:22:50 UTC |
| e789887 | jdaeth274 | 13 August 2021, 16:11:48 UTC | checking intermediate file names | 13 August 2021, 16:11:48 UTC |
| c7ee386 | jdaeth274 | 13 August 2021, 14:22:26 UTC | getting the output file | 13 August 2021, 14:22:26 UTC |
| b458e54 | jdaeth274 | 13 August 2021, 09:37:31 UTC | tweaking the output files | 13 August 2021, 09:37:31 UTC |
| b75f04e | jdaeth274 | 10 August 2021, 17:48:32 UTC | tweaking intermediates | 10 August 2021, 17:48:32 UTC |
| 351ac93 | jdaeth274 | 06 August 2021, 17:27:01 UTC | adding in function to remove internal nodes from raxmlng alignment | 06 August 2021, 17:27:01 UTC |
| ce29a58 | jdaeth274 | 06 August 2021, 16:43:40 UTC | adding in function to remove internal nodes from raxmlng alignment | 06 August 2021, 16:43:40 UTC |
| 48128ab | jdaeth274 | 04 August 2021, 10:59:45 UTC | Adding in function to remove hashes and colons from seq names | 04 August 2021, 10:59:45 UTC |
| 078d716 | Croucher | 27 July 2021, 20:37:35 UTC | Allow for safe sys.exit | 27 July 2021, 20:37:35 UTC |
| 86d2226 | Croucher | 27 July 2021, 20:37:35 UTC | Allow for safe sys.exit | 27 July 2021, 20:37:35 UTC |
| 0a7f3e2 | Croucher | 27 July 2021, 05:39:27 UTC | Specify threads for raxml-ng | 27 July 2021, 05:39:27 UTC |
| 32b1478 | Croucher | 27 July 2021, 05:39:27 UTC | Specify threads for raxml-ng | 27 July 2021, 05:39:27 UTC |
| 32bf544 | nickjcroucher | 18 May 2021, 12:17:44 UTC | Simplify selection of multithreaded raxml-ng | 18 May 2021, 12:17:44 UTC |
| b4a06a3 | nickjcroucher | 18 May 2021, 12:17:44 UTC | Simplify selection of multithreaded raxml-ng | 18 May 2021, 12:17:44 UTC |
| b576ae5 | nickjcroucher | 18 May 2021, 12:09:24 UTC | Enable selection of multithreaded raxml-ng | 18 May 2021, 12:09:24 UTC |
| f19b739 | nickjcroucher | 18 May 2021, 12:09:24 UTC | Enable selection of multithreaded raxml-ng | 18 May 2021, 12:09:24 UTC |
| 1d5d05a | nickjcroucher | 13 May 2021, 11:15:20 UTC | Add script for extracting sequence subsets | 13 May 2021, 11:15:20 UTC |
| b61a4b0 | nickjcroucher | 13 May 2021, 11:15:20 UTC | Add script for extracting sequence subsets | 13 May 2021, 11:15:20 UTC |
| 22cac14 | nickjcroucher | 07 May 2021, 17:03:49 UTC | Script for generating an input alignment using SKA | 07 May 2021, 17:03:49 UTC |
| 825bd25 | nickjcroucher | 07 May 2021, 17:03:49 UTC | Script for generating an input alignment using SKA | 07 May 2021, 17:03:49 UTC |
| 23076fd | nickjcroucher | 06 May 2021, 09:06:04 UTC | Add script for masking recombinant regions | 06 May 2021, 09:06:04 UTC |
| a364acb | nickjcroucher | 06 May 2021, 09:06:04 UTC | Add script for masking recombinant regions | 06 May 2021, 09:06:04 UTC |
| 25184cf | Christoph Püthe | 29 January 2021, 16:16:24 UTC | add workflow name for github badge | 29 January 2021, 16:16:24 UTC |
| 7c08577 | Christoph Püthe | 29 January 2021, 16:16:24 UTC | add workflow name for github badge | 29 January 2021, 16:16:24 UTC |
| 2be742a | Christoph Püthe | 29 January 2021, 14:52:57 UTC | Merge pull request #294 from sanger-pathogens/dockerandci get CI and Docker build running | 29 January 2021, 14:52:57 UTC |
| 5200eb2 | Christoph Püthe | 29 January 2021, 14:52:57 UTC | Merge pull request #294 from sanger-pathogens/dockerandci get CI and Docker build running | 29 January 2021, 14:52:57 UTC |
| 008fee3 | puethe | 29 January 2021, 14:41:52 UTC | get CI and Docker build running | 29 January 2021, 14:41:52 UTC |
| 05f6b3c | puethe | 29 January 2021, 14:41:52 UTC | get CI and Docker build running | 29 January 2021, 14:41:52 UTC |
| 0497efd | nickjcroucher | 28 January 2021, 22:38:53 UTC | Merge pull request #293 from sanger-pathogens/fixdocker Update creation of Dockerfile | 28 January 2021, 22:38:53 UTC |
| aad6897 | nickjcroucher | 28 January 2021, 22:38:53 UTC | Merge pull request #293 from sanger-pathogens/fixdocker Update creation of Dockerfile | 28 January 2021, 22:38:53 UTC |
| 61302b2 | nickjcroucher | 28 January 2021, 19:51:34 UTC | Further edit to RAxML selection function | 28 January 2021, 19:51:34 UTC |
| ed3601f | nickjcroucher | 28 January 2021, 19:51:34 UTC | Further edit to RAxML selection function | 28 January 2021, 19:51:34 UTC |
| 4f06dbe | nickjcroucher | 28 January 2021, 19:41:37 UTC | Restore RAxML selection function | 28 January 2021, 19:41:37 UTC |
| e98092f | nickjcroucher | 28 January 2021, 19:41:37 UTC | Restore RAxML selection function | 28 January 2021, 19:41:37 UTC |
| 7f91063 | nickjcroucher | 28 January 2021, 19:28:30 UTC | Alter RAxML selection function | 28 January 2021, 19:28:30 UTC |
| afba6b5 | nickjcroucher | 28 January 2021, 19:28:30 UTC | Alter RAxML selection function | 28 January 2021, 19:28:30 UTC |
| be29846 | puethe | 28 January 2021, 18:12:45 UTC | working Dockerfile based on pytest | 28 January 2021, 18:12:45 UTC |
| f0d30f1 | puethe | 28 January 2021, 18:12:45 UTC | working Dockerfile based on pytest | 28 January 2021, 18:12:45 UTC |
| 172d435 | puethe | 28 January 2021, 17:31:13 UTC | workflow back to original | 28 January 2021, 17:31:13 UTC |
| 58c2009 | puethe | 28 January 2021, 17:31:13 UTC | workflow back to original | 28 January 2021, 17:31:13 UTC |
| 96755d9 | puethe | 28 January 2021, 17:21:03 UTC | add coverage back | 28 January 2021, 17:21:03 UTC |
| c27e1da | puethe | 28 January 2021, 17:21:03 UTC | add coverage back | 28 January 2021, 17:21:03 UTC |
| 462e37c | puethe | 28 January 2021, 17:06:50 UTC | pure pytest | 28 January 2021, 17:06:50 UTC |
| db46ba7 | puethe | 28 January 2021, 17:06:50 UTC | pure pytest | 28 January 2021, 17:06:50 UTC |
| 67b9712 | puethe | 28 January 2021, 15:50:52 UTC | improve choosing executable by processor | 28 January 2021, 15:50:52 UTC |
| d89a468 | puethe | 28 January 2021, 15:50:52 UTC | improve choosing executable by processor | 28 January 2021, 15:50:52 UTC |
| 86f0856 | puethe | 28 January 2021, 14:35:32 UTC | try with sudo | 28 January 2021, 14:35:32 UTC |
| e1fdc88 | puethe | 28 January 2021, 14:35:32 UTC | try with sudo | 28 January 2021, 14:35:32 UTC |
| 1cfccfb | puethe | 28 January 2021, 12:25:17 UTC | get Docker working | 28 January 2021, 12:25:17 UTC |
