| HEAD | f571b77 | Enlarge logo | 01 December 2023, 13:14:37 UTC |
| refs/heads/149_no_filter_dups | a6e9221 | back port changes to not filter duplicate sequences by default | 31 October 2016, 13:28:06 UTC |
| refs/heads/JAR | c39c39f | Replaced RAxML sequence reconstruction with python joint ancestral reconstruction | 25 January 2018, 14:18:19 UTC |
| refs/heads/alignment_updating | c2d0ac0 | Update for new alignment generation | 05 May 2023, 06:56:28 UTC |
| refs/heads/c_mem | b2554d0 | Increase threshold for patches | 19 January 2022, 15:40:59 UTC |
| refs/heads/conda_patch | 4cee609 | Reverse patch changes to configure This reverts commit aa14e1f70e6a924d3af5102a11075a4532928a6f. | 18 September 2023, 04:33:57 UTC |
| refs/heads/fix_installation | 9d1c604 | Revert version constriants | 13 March 2024, 21:20:12 UTC |
| refs/heads/fix_tests | 2f9f80c | Merge branch 'fix_tests' of https://github.com/sanger-pathogens/gubbins into fix_tests | 02 March 2022, 09:16:34 UTC |
| refs/heads/fixdocker | ed3601f | Further edit to RAxML selection function | 28 January 2021, 19:51:34 UTC |
| refs/heads/gh-pages | b9478c4 | Fix alignment of code | 19 January 2022, 13:00:42 UTC |
| refs/heads/hpc_fix | 2ebecea | Remove build directory | 06 October 2021, 09:58:05 UTC |
| refs/heads/improve_scripts | 0dfe123 | Merge and improve clade analysis scripts | 31 October 2022, 05:28:42 UTC |
| refs/heads/improve_testing | 1a00506 | Improve dependency testing | 21 December 2021, 12:00:03 UTC |
| refs/heads/jdaeth274-josh_merging_branch | 25ee999 | Resolve ska script conflict | 22 February 2022, 07:51:13 UTC |
| refs/heads/masking_aln | b85e832 | Bump version | 06 October 2021, 20:51:16 UTC |
| refs/heads/master | f571b77 | Enlarge logo | 01 December 2023, 13:14:37 UTC |
| refs/heads/new_ska2 | 1b689a7 | Fix broken link | 11 September 2023, 05:42:05 UTC |
| refs/heads/numpyjar | 97591ce | Update changelog for v3.1.4 | 15 November 2021, 11:20:44 UTC |
| refs/heads/raxml_reconstruction | ccd5449 | Merge pull request #171 from andrewjpage/raxml_reconstruction Raxml reconstruction | 15 July 2016, 17:09:37 UTC |
| refs/heads/rec_per_gene | 0b19f91 | Fix python rec counting script command | 08 March 2023, 10:15:54 UTC |
| refs/heads/star_fix | cfc181c | tweaking pyjar | 29 April 2022, 08:07:00 UTC |
| refs/heads/time_tree | 079d890 | Add correct reference files | 06 October 2022, 09:10:49 UTC |
| refs/heads/update_rec | 4d296db | Add validation of datasets being combined | 14 July 2022, 09:58:06 UTC |
| refs/tags/0.1.10 | cae13d8 | Merge pull request #103 from andrewjpage/print_excluded_sequences print list of excluded sequences | 22 August 2014, 13:46:31 UTC |
| refs/tags/0.1.11 | 7e6bd0d | Merge pull request #105 from andrewjpage/print_excluded_sequences version in configure | 22 August 2014, 15:49:59 UTC |
| refs/tags/0.1.6 | 1caef95 | Merge pull request #99 from andrewjpage/master Changes from Aidan Delaney | 12 August 2014, 12:39:40 UTC |
| refs/tags/0.1.7 | 7b601c8 | Merge pull request #100 from andrewjpage/master Build for trusty | 14 August 2014, 14:35:45 UTC |
| refs/tags/0.1.8 | e0f5498 | Merge pull request #101 from andrewjpage/fasttree_exec Fasttree exec | 15 August 2014, 15:35:09 UTC |
| refs/tags/0.1.9 | 89faac9 | Merge pull request #102 from andrewjpage/master print errors for invalid input files | 22 August 2014, 09:46:14 UTC |
| refs/tags/0.2 | 155d08a | Merge pull request #106 from andrewjpage/catch_too_few_sequences Catch too few sequences | 02 September 2014, 08:29:19 UTC |
| refs/tags/0.6 | 7a929bd | Update README.md | 24 September 2014, 08:22:03 UTC |
| refs/tags/0.7 | 7a929bd | Update README.md | 24 September 2014, 08:22:03 UTC |
| refs/tags/1.0.9 | 7fc9389 | Merge pull request #122 from andrewjpage/cpu_info Dont use cpu info to find the flags | 06 January 2015, 15:18:37 UTC |
| refs/tags/v.1.4.5 | c5c8dec | Merge pull request #160 from andrewjpage/remove_install_sh remove install-sh | 13 January 2016, 11:31:14 UTC |
| refs/tags/v0.3 | 18feeee | Change stats output format and don't delete fastml tree | 04 September 2014, 16:08:16 UTC |
| refs/tags/v0.4 | 6b496da | Merge pull request #108 from andrewjpage/pairwise_rename_files pairwise rename output files | 05 September 2014, 09:30:33 UTC |
| refs/tags/v0.4.1 | e5b92fb | Merge pull request #109 from andrewjpage/master Check for lowercase fasttree exec | 08 September 2014, 09:42:18 UTC |
| refs/tags/v0.5 | 62eda04 | Merge pull request #110 from andrewjpage/master thread support for raxml | 09 September 2014, 08:51:56 UTC |
| refs/tags/v0.6 | 54d9985 | Merge pull request #111 from andrewjpage/master Gubbins drawer can use recombination embl file | 09 September 2014, 12:26:00 UTC |
| refs/tags/v1.0 | 2b0c0f3 | Merge pull request #112 from andrewjpage/converging_recombinations Converging recombinations | 14 October 2014, 13:21:59 UTC |
| refs/tags/v1.0.1 | adc5944 | change log | 14 October 2014, 14:21:30 UTC |
| refs/tags/v1.0.10 | 10874c1 | check if raxml files exist and print error | 19 January 2015, 09:37:38 UTC |
| refs/tags/v1.0.11 | 68c58e0 | force upload to ppa | 19 January 2015, 13:14:07 UTC |
| refs/tags/v1.0.12 | 5f07d92 | Merge pull request #125 from andrewjpage/remove_internal_nodes_from_final_tree test data | 20 January 2015, 09:10:33 UTC |
| refs/tags/v1.0.2 | 649cc65 | Merge pull request #114 from andrewjpage/rename_converge_method rename convergence methods and allow for more | 16 October 2014, 10:55:57 UTC |
| refs/tags/v1.0.5 | 30f3a10 | Merge pull request #117 from andrewjpage/fasttree fasttree executables with titlecase and lowercase | 19 November 2014, 16:50:24 UTC |
| refs/tags/v1.0.6 | 6f53c39 | allow for variation and exclude zero track length | 03 December 2014, 10:36:53 UTC |
| refs/tags/v1.0.7 | 6a054d2 | check more iterations in test for prev seen recombinations | 08 December 2014, 14:29:41 UTC |
| refs/tags/v1.0.8 | fb730e8 | class namespace | 08 December 2014, 15:25:03 UTC |
| refs/tags/v1.0.9 | 7fc9389 | Merge pull request #122 from andrewjpage/cpu_info Dont use cpu info to find the flags | 06 January 2015, 15:18:37 UTC |
| refs/tags/v1.1.0 | d06e3fd | make tests past split | 23 January 2015, 15:27:19 UTC |
| refs/tags/v1.1.1 | 6499829 | message about invalid outgroups | 23 January 2015, 16:02:50 UTC |
| refs/tags/v1.1.2 | 4b7486a | Merge pull request #128 from andrewjpage/update_robustness Update robustness | 06 March 2015, 11:30:39 UTC |
| refs/tags/v1.2.0 | 4b7486a | Merge pull request #128 from andrewjpage/update_robustness Update robustness | 06 March 2015, 11:30:39 UTC |
| refs/tags/v1.2.1 | 7b597ff | Merge pull request #133 from andrewjpage/correct_vcf_format Correct vcf format and EMBL format | 30 March 2015, 10:37:55 UTC |
| refs/tags/v1.2.2 | 6ec565c | include last element of array | 30 March 2015, 13:18:11 UTC |
| refs/tags/v1.2.3 | bdd1854 | Merge branch 'master' of github.com:sanger-pathogens/gubbins | 30 March 2015, 13:59:12 UTC |
| refs/tags/v1.2.4 | 4d193d8 | Merge pull request #135 from andrewjpage/script_version_number output version in python script | 31 March 2015, 14:02:24 UTC |
| refs/tags/v1.3.0 | b5b73f6 | Merge pull request #137 from andrewjpage/recalculate_genome_length Recalculate genome length | 16 April 2015, 14:32:03 UTC |
| refs/tags/v1.3.1 | 5f9c17e | Merge pull request #138 from andrewjpage/recalculate_genome_length version 1.3.1 | 16 April 2015, 14:33:56 UTC |
| refs/tags/v1.3.3 | 75e5a84 | Merge pull request #140 from andrewjpage/window_size_self_error Window size self error | 16 April 2015, 15:10:13 UTC |
| refs/tags/v1.3.4 | afb6460 | inc version | 18 May 2015, 13:50:03 UTC |
| refs/tags/v1.4.0 | 21757dc | Merge pull request #149 from andrewjpage/convert_python_to_3 Convert python to 3 | 01 July 2015, 15:41:09 UTC |
| refs/tags/v1.4.1 | 0d0bb60 | update version | 07 July 2015, 14:39:54 UTC |
| refs/tags/v1.4.10 | a6e9221 | back port changes to not filter duplicate sequences by default | 31 October 2016, 13:28:06 UTC |
| refs/tags/v1.4.2 | a81dbbe | Merge pull request #153 from andrewjpage/filename_length check for input files which are too long | 02 September 2015, 15:07:47 UTC |
| refs/tags/v1.4.3 | 0e3b263 | update version | 19 November 2015, 10:02:23 UTC |
| refs/tags/v1.4.4 | 336f824 | linux only library | 09 December 2015, 15:43:56 UTC |
| refs/tags/v1.4.5 | c5c8dec | Merge pull request #160 from andrewjpage/remove_install_sh remove install-sh | 13 January 2016, 11:31:14 UTC |
| refs/tags/v1.4.6 | bcc3b87 | update version | 29 February 2016, 15:19:27 UTC |
| refs/tags/v1.4.7 | e2adff3 | update version | 29 February 2016, 16:16:22 UTC |
| refs/tags/v1.4.8 | 677be48 | update version number | 13 April 2016, 09:59:20 UTC |
| refs/tags/v1.4.9 | a4b6c1d | Merge pull request #166 from andrewjpage/duplicate_sequences Duplicate sequences | 15 April 2016, 12:27:52 UTC |
| refs/tags/v2.0.0 | a5f4fc0 | Merge pull request #172 from andrewjpage/raxml_reconstruction Raxml reconstruction | 15 July 2016, 17:13:08 UTC |
| refs/tags/v2.1.0 | 99d6756 | Merge pull request #175 from andrewjpage/speedup Use GTRCAT by default with RAxML | 22 July 2016, 13:32:22 UTC |
| refs/tags/v2.2.0 | 5bb1896 | 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 |
| refs/tags/v2.2.1 | 1d13185 | Merge pull request #193 from ssjunnebo/master updated manual | 02 August 2017, 12:10:44 UTC |
| refs/tags/v2.2.2 | b907ad4 | allow for AVX2 | 04 September 2017, 10:05:21 UTC |
| refs/tags/v2.2.3 | 3ad41e8 | Merge pull request #200 from andrewjpage/helptext Fix default extended help text. | 15 September 2017, 13:04:25 UTC |
| refs/tags/v2.3.0 | dbe0b71 | Merge pull request #201 from andrewjpage/gubbins_drawer_help Gubbins drawer help text | 21 September 2017, 14:33:23 UTC |
| refs/tags/v2.3.1 | b7b935d | Merge branch 'internal_nodes' | 22 September 2017, 10:57:33 UTC |
| refs/tags/v2.3.2 | 2856b5e | Merge pull request #221 from puethe/remove_gubbins_drawer Replaced the script gubbins_drawer.py with an empty script displaying an info message. | 15 June 2018, 11:48:19 UTC |
| refs/tags/v2.3.3 | e1b4ec6 | Merge pull request #226 from puethe/independent_docker Dockerfile independent from debian package | 26 July 2018, 16:03:35 UTC |
| refs/tags/v2.3.4 | e1df9fe | Merge pull request #227 from puethe/segfault dynamically allocate memory to avoid stack overflow | 30 July 2018, 15:30:49 UTC |
| refs/tags/v2.3.5 | ed228dc | Merge pull request #261 from puethe/master update changelog | 11 November 2019, 18:09:01 UTC |
| refs/tags/v2.4.0 | ffeaa9e | Merge pull request #265 from smoe/patch-1 Removed autogenerated files from source tree | 03 January 2020, 17:18:45 UTC |
| refs/tags/v2.4.0-docker2 | 5177ce2 | Merge pull request #269 from puethe/gdb adding gdb to Dockerfile | 13 January 2020, 15:46:24 UTC |
| refs/tags/v2.4.1 | afc51e6 | Merge pull request #271 from sanger-pathogens/gdb Fix memory leaks | 20 January 2020, 10:25:33 UTC |
| refs/tags/v3.0.0 | 25184cf | add workflow name for github badge | 29 January 2021, 16:16:24 UTC |
| refs/tags/v3.1.0 | 3db99f5 | Merge pull request #305 from sanger-pathogens/masking_aln Version 3.1 | 06 October 2021, 21:13:00 UTC |
| refs/tags/v3.1.1 | a051f2e | Merge pull request #310 from sanger-pathogens/raxmlng_fix Fix to RAxML-NG | 12 October 2021, 06:19:10 UTC |
| refs/tags/v3.1.2 | 4a7ae96 | Merge pull request #311 from jdaeth274/masking_aln Only write aln if names change | 12 October 2021, 10:26:04 UTC |
| refs/tags/v3.1.3 | 33acd75 | Update change log for v3.1.3 | 22 October 2021, 07:51:05 UTC |
| refs/tags/v3.1.4 | 12ceb14 | Merge pull request #319 from sanger-pathogens/numpyjar Reimplement JAR with numpy and numba | 15 November 2021, 11:35:55 UTC |
| refs/tags/v3.1.5 | 7f41109 | Merge pull request #328 from nickjcroucher/c_mem Improvements to reconstruction algorithm | 19 January 2022, 15:54:16 UTC |
| refs/tags/v3.1.6 | 4e4f061 | Merge pull request #329 from nickjcroucher/recon_fix Add tests for reconstruction accuracy | 20 January 2022, 08:59:40 UTC |
| refs/tags/v3.2.0 | a9d5dcd | Merge pull request #334 from nickjcroucher/fix_tests Fixes to ensure code passes CI tests | 02 March 2022, 17:16:28 UTC |
| refs/tags/v3.2.1 | eb7b75e | Merge pull request #338 from nickjcroucher/update_rec v3.2.1 | 24 May 2022, 10:00:59 UTC |
| refs/tags/v3.2.2 | 89a1e55 | Merge pull request #389 from nickjcroucher/add_seed Enable seed specification | 30 November 2023, 18:55:09 UTC |
| refs/tags/v3.3 | b83a607 | Merge pull request #350 from nickjcroucher/time_tree Merge in capacity to generate time-calibrated trees | 06 October 2022, 09:46:06 UTC |
