| 4b7486a | andrewjpage | 06 March 2015, 11:30:39 UTC | Merge pull request #128 from andrewjpage/update_robustness Update robustness | 06 March 2015, 11:30:39 UTC |
| 5cbe0f7 | andrewjpage | 06 March 2015, 11:29:30 UTC | Fix warnings | 06 March 2015, 11:29:30 UTC |
| c2fab08 | andrewjpage | 06 March 2015, 09:46:24 UTC | fix gff format and better error messages | 06 March 2015, 09:46:24 UTC |
| c3daaaa | andrewjpage | 26 January 2015, 10:21:52 UTC | make sure ntp is available | 26 January 2015, 10:21:52 UTC |
| 5fb9599 | andrewjpage | 26 January 2015, 10:04:05 UTC | further debian changelog syntax fix | 26 January 2015, 10:04:05 UTC |
| 49ef9ae | andrewjpage | 26 January 2015, 10:00:51 UTC | fix debian changelog syntax | 26 January 2015, 10:00:51 UTC |
| 9aad71c | andrewjpage | 23 January 2015, 16:03:08 UTC | Merge pull request #127 from andrewjpage/error_message_with_outgroup_not_clade message about invalid outgroups | 23 January 2015, 16:03:08 UTC |
| 6499829 | andrewjpage | 23 January 2015, 16:02:50 UTC | message about invalid outgroups | 23 January 2015, 16:02:50 UTC |
| 404203e | andrewjpage | 23 January 2015, 15:27:40 UTC | Merge pull request #126 from andrewjpage/clade_as_outgroup Clade as outgroup | 23 January 2015, 15:27:40 UTC |
| d06e3fd | andrewjpage | 23 January 2015, 15:27:19 UTC | make tests past split | 23 January 2015, 15:27:19 UTC |
| 5450158 | andrewjpage | 23 January 2015, 15:06:13 UTC | allow for multiple outgroups | 23 January 2015, 15:06:13 UTC |
| 5f07d92 | andrewjpage | 20 January 2015, 09:10:33 UTC | Merge pull request #125 from andrewjpage/remove_internal_nodes_from_final_tree test data | 20 January 2015, 09:10:33 UTC |
| 9e2dd9c | andrewjpage | 20 January 2015, 09:09:12 UTC | test data | 20 January 2015, 09:09:12 UTC |
| 6353400 | andrewjpage | 20 January 2015, 09:06:02 UTC | Merge pull request #124 from andrewjpage/remove_internal_nodes_from_final_tree Remove internal nodes from final tree | 20 January 2015, 09:06:02 UTC |
| 8005e71 | andrewjpage | 20 January 2015, 09:04:34 UTC | version 1.0.12 | 20 January 2015, 09:04:34 UTC |
| d706918 | andrewjpage | 20 January 2015, 09:02:52 UTC | remove internal labels from final tree | 20 January 2015, 09:02:52 UTC |
| 68c58e0 | andrewjpage | 19 January 2015, 13:14:07 UTC | force upload to ppa | 19 January 2015, 13:14:07 UTC |
| fd80ebd | andrewjpage | 19 January 2015, 09:42:08 UTC | Merge pull request #123 from andrewjpage/master check fasta files valid and check for intermediate raxml files | 19 January 2015, 09:42:08 UTC |
| 10874c1 | andrewjpage | 19 January 2015, 09:37:38 UTC | check if raxml files exist and print error | 19 January 2015, 09:37:38 UTC |
| 5ee8bd8 | andrewjpage | 19 January 2015, 09:01:57 UTC | test intermediate fasta file is valid after fastml | 19 January 2015, 09:01:57 UTC |
| 739bcfb | andrewjpage | 16 January 2015, 16:07:44 UTC | check the input sequences contain some variation | 16 January 2015, 16:07:44 UTC |
| 395774c | andrewjpage | 08 January 2015, 10:05:43 UTC | remove markdown around data | 08 January 2015, 10:05:43 UTC |
| 0c17f31 | andrewjpage | 08 January 2015, 09:56:06 UTC | link to Gubbins webpage in install file | 08 January 2015, 09:56:06 UTC |
| 3eb6cce | andrewjpage | 08 January 2015, 09:46:12 UTC | paper and dataset to read me | 08 January 2015, 09:46:12 UTC |
| 7fc9389 | andrewjpage | 06 January 2015, 15:18:37 UTC | Merge pull request #122 from andrewjpage/cpu_info Dont use cpu info to find the flags | 06 January 2015, 15:18:37 UTC |
| 98469b6 | andrewjpage | 06 January 2015, 15:04:02 UTC | BioPhylo default branch lengths changed | 06 January 2015, 15:04:02 UTC |
| 482db31 | andrewjpage | 06 January 2015, 14:11:50 UTC | manually check cpu flags | 06 January 2015, 14:11:50 UTC |
| 6fce94a | andrewjpage | 08 December 2014, 15:25:32 UTC | Merge pull request #121 from andrewjpage/linux_only_cpu_info class namespace | 08 December 2014, 15:25:32 UTC |
| fb730e8 | andrewjpage | 08 December 2014, 15:25:03 UTC | class namespace | 08 December 2014, 15:25:03 UTC |
| 8d6fd81 | andrewjpage | 08 December 2014, 15:16:39 UTC | Merge pull request #120 from andrewjpage/linux_only_cpu_info reduced functionality but more stable cpu info lookup | 08 December 2014, 15:16:39 UTC |
| e54c5aa | andrewjpage | 08 December 2014, 15:14:24 UTC | reduced functionality but more stable cpu info lookup | 08 December 2014, 15:15:36 UTC |
| 1b6b1f0 | andrewjpage | 08 December 2014, 14:32:48 UTC | Merge pull request #119 from andrewjpage/rho_theta Rho theta | 08 December 2014, 14:32:48 UTC |
| 6a054d2 | andrewjpage | 08 December 2014, 14:29:41 UTC | check more iterations in test for prev seen recombinations | 08 December 2014, 14:29:41 UTC |
| c26a3d9 | andrewjpage | 08 December 2014, 14:22:57 UTC | use continue rather than next | 08 December 2014, 14:22:57 UTC |
| c9174d1 | andrewjpage | 08 December 2014, 14:03:14 UTC | check cpu flags for raxml | 08 December 2014, 14:03:14 UTC |
| 296af56 | andrewjpage | 08 December 2014, 12:59:19 UTC | update rho theta calculation | 08 December 2014, 12:59:43 UTC |
| f004fbf | andrewjpage | 03 December 2014, 11:34:08 UTC | changelog_update | 03 December 2014, 11:34:08 UTC |
| 0658d6b | andrewjpage | 03 December 2014, 10:38:28 UTC | Merge pull request #118 from andrewjpage/gubbins_drawer_snps allow for variation and exclude zero track length | 03 December 2014, 10:38:28 UTC |
| 6f53c39 | andrewjpage | 03 December 2014, 10:36:53 UTC | allow for variation and exclude zero track length | 03 December 2014, 10:36:53 UTC |
| 30f3a10 | andrewjpage | 19 November 2014, 16:50:24 UTC | Merge pull request #117 from andrewjpage/fasttree fasttree executables with titlecase and lowercase | 19 November 2014, 16:50:24 UTC |
| f142cec | andrewjpage | 19 November 2014, 16:50:02 UTC | fasttree executables with titlecase and lowercase | 19 November 2014, 16:50:02 UTC |
| bc277a3 | andrewjpage | 14 November 2014, 13:11:59 UTC | Merge pull request #116 from andrewjpage/change_raxml_exec_search_order warning message when changing number of threads | 14 November 2014, 13:11:59 UTC |
| 05ba0b3 | andrewjpage | 14 November 2014, 13:10:46 UTC | warning message when changing number of threads | 14 November 2014, 13:10:46 UTC |
| a8f7e2a | andrewjpage | 14 November 2014, 11:08:03 UTC | Merge pull request #115 from andrewjpage/change_raxml_exec_search_order Change raxml exec search order | 14 November 2014, 11:08:03 UTC |
| 3221a02 | andrewjpage | 14 November 2014, 11:07:32 UTC | raxml PTHREADS needs 2 or more threads, however some systems dont come with the single threaded exec | 14 November 2014, 11:07:32 UTC |
| 5dab100 | andrewjpage | 14 November 2014, 10:23:43 UTC | change search order of raxml and default to 1 thread | 14 November 2014, 10:23:43 UTC |
| 649cc65 | andrewjpage | 16 October 2014, 10:55:57 UTC | Merge pull request #114 from andrewjpage/rename_converge_method rename convergence methods and allow for more | 16 October 2014, 10:55:57 UTC |
| 9b40ae7 | andrewjpage | 16 October 2014, 10:55:07 UTC | rename convergence methods and allow for more | 16 October 2014, 10:55:07 UTC |
| 4a31d54 | andrewjpage | 14 October 2014, 14:30:54 UTC | Merge branch 'master' of github.com:sanger-pathogens/gubbins | 14 October 2014, 14:30:54 UTC |
| adc5944 | andrewjpage | 14 October 2014, 14:21:30 UTC | change log | 14 October 2014, 14:21:30 UTC |
| 7ab9a74 | andrewjpage | 14 October 2014, 14:12:33 UTC | missing test file | 14 October 2014, 14:12:33 UTC |
| 4f007da | andrewjpage | 14 October 2014, 13:34:50 UTC | Merge pull request #113 from andrewjpage/master unstable test fixed | 14 October 2014, 13:34:50 UTC |
| 8dace05 | andrewjpage | 14 October 2014, 13:34:33 UTC | unstable test fixed | 14 October 2014, 13:34:33 UTC |
| 2b0c0f3 | andrewjpage | 14 October 2014, 13:21:59 UTC | Merge pull request #112 from andrewjpage/converging_recombinations Converging recombinations | 14 October 2014, 13:21:59 UTC |
| 69a1900 | andrewjpage | 14 October 2014, 13:21:29 UTC | allow for strict convergence | 14 October 2014, 13:21:29 UTC |
| bee062c | andrewjpage | 14 October 2014, 09:22:20 UTC | get recombinations from embl file | 14 October 2014, 09:22:20 UTC |
| 1c10169 | andrewjpage | 14 October 2014, 08:17:18 UTC | Merge branch 'master' of github.com:sanger-pathogens/gubbins | 14 October 2014, 08:17:18 UTC |
| 7a929bd | andrewjpage | 24 September 2014, 08:22:03 UTC | Update README.md | 24 September 2014, 08:22:03 UTC |
| 23af202 | andrewjpage | 17 September 2014, 13:52:03 UTC | update install instructions | 17 September 2014, 13:52:03 UTC |
| 5488dab | andrewjpage | 09 September 2014, 14:59:42 UTC | homebrew | 09 September 2014, 14:59:42 UTC |
| 54d9985 | andrewjpage | 09 September 2014, 12:26:00 UTC | Merge pull request #111 from andrewjpage/master Gubbins drawer can use recombination embl file | 09 September 2014, 12:26:00 UTC |
| 78303dd | andrewjpage | 09 September 2014, 12:04:32 UTC | Gubbins drawer can use recombination embl file | 09 September 2014, 12:04:32 UTC |
| 5801e20 | andrewjpage | 09 September 2014, 11:40:47 UTC | Read version number from one place | 09 September 2014, 11:40:47 UTC |
| 62eda04 | andrewjpage | 09 September 2014, 08:51:56 UTC | Merge pull request #110 from andrewjpage/master thread support for raxml | 09 September 2014, 08:51:56 UTC |
| 059fe0c | andrewjpage | 09 September 2014, 08:49:41 UTC | thread support for raxml | 09 September 2014, 08:49:41 UTC |
| e5b92fb | andrewjpage | 08 September 2014, 09:42:18 UTC | Merge pull request #109 from andrewjpage/master Check for lowercase fasttree exec | 08 September 2014, 09:42:18 UTC |
| 572569c | andrewjpage | 08 September 2014, 09:41:30 UTC | Check for lowercase version of fast tree exec | 08 September 2014, 09:41:30 UTC |
| 3bf6aac | andrewjpage | 08 September 2014, 08:20:57 UTC | change email address and readme | 08 September 2014, 08:20:57 UTC |
| 6b496da | andrewjpage | 05 September 2014, 09:30:33 UTC | Merge pull request #108 from andrewjpage/pairwise_rename_files pairwise rename output files | 05 September 2014, 09:30:33 UTC |
| a9a73d8 | andrewjpage | 05 September 2014, 09:30:09 UTC | pairwise rename output files | 05 September 2014, 09:30:09 UTC |
| eafa6bd | andrewjpage | 04 September 2014, 16:09:30 UTC | Merge pull request #107 from andrewjpage/update_stats_headers Update stats headers | 04 September 2014, 16:09:30 UTC |
| 18feeee | andrewjpage | 04 September 2014, 16:08:16 UTC | Change stats output format and don't delete fastml tree | 04 September 2014, 16:08:16 UTC |
| 8732277 | andrewjpage | 02 September 2014, 13:08:29 UTC | move install to another file | 02 September 2014, 13:08:29 UTC |
| 155d08a | andrewjpage | 02 September 2014, 08:29:19 UTC | Merge pull request #106 from andrewjpage/catch_too_few_sequences Catch too few sequences | 02 September 2014, 08:29:19 UTC |
| 9151f5a | andrewjpage | 02 September 2014, 08:28:15 UTC | update to version 0.2 | 02 September 2014, 08:28:15 UTC |
| 1909cad | andrewjpage | 01 September 2014, 10:50:09 UTC | rename the output files to more meaningful names | 01 September 2014, 10:50:09 UTC |
| 97abcea | andrewjpage | 01 September 2014, 10:23:32 UTC | lookup tables for translating to final names plus prefix | 01 September 2014, 10:23:32 UTC |
| 1c3f3b1 | andrewjpage | 01 September 2014, 09:47:51 UTC | delete temp files from fastml | 01 September 2014, 09:47:51 UTC |
| 7404620 | andrewjpage | 27 August 2014, 12:34:38 UTC | fix uncommented tests | 27 August 2014, 12:34:38 UTC |
| ea26d93 | andrewjpage | 27 August 2014, 12:25:42 UTC | if you have less than 4 sequences you cant build a tree with raxml | 27 August 2014, 12:25:42 UTC |
| 7e6bd0d | andrewjpage | 22 August 2014, 15:49:59 UTC | Merge pull request #105 from andrewjpage/print_excluded_sequences version in configure | 22 August 2014, 15:49:59 UTC |
| fc07f88 | andrewjpage | 22 August 2014, 15:49:43 UTC | version in configure | 22 August 2014, 15:49:43 UTC |
| 4350943 | andrewjpage | 22 August 2014, 15:45:36 UTC | Merge pull request #104 from andrewjpage/print_excluded_sequences Support for bipartition trees as input | 22 August 2014, 15:45:36 UTC |
| c0ce86e | andrewjpage | 22 August 2014, 15:44:45 UTC | Support for bipartition trees as input | 22 August 2014, 15:44:45 UTC |
| cae13d8 | andrewjpage | 22 August 2014, 13:46:31 UTC | Merge pull request #103 from andrewjpage/print_excluded_sequences print list of excluded sequences | 22 August 2014, 13:46:31 UTC |
| 88103d2 | andrewjpage | 22 August 2014, 13:46:08 UTC | print list of excluded sequences | 22 August 2014, 13:46:08 UTC |
| 89faac9 | andrewjpage | 22 August 2014, 09:46:14 UTC | Merge pull request #102 from andrewjpage/master print errors for invalid input files | 22 August 2014, 09:46:14 UTC |
| 20268db | andrewjpage | 22 August 2014, 09:42:18 UTC | print errors for invalid input files | 22 August 2014, 09:42:18 UTC |
| e0f5498 | andrewjpage | 15 August 2014, 15:35:09 UTC | Merge pull request #101 from andrewjpage/fasttree_exec Fasttree exec | 15 August 2014, 15:35:09 UTC |
| 587f12c | andrewjpage | 15 August 2014, 15:34:50 UTC | version 0.1.8 | 15 August 2014, 15:34:50 UTC |
| 777524f | andrewjpage | 15 August 2014, 15:29:44 UTC | test for checking if names in fasta match tree | 15 August 2014, 15:29:44 UTC |
| 13991e5 | andrewjpage | 15 August 2014, 15:16:30 UTC | fasttree exec and taxon name check | 15 August 2014, 15:16:30 UTC |
| 7b601c8 | andrewjpage | 14 August 2014, 14:35:45 UTC | Merge pull request #100 from andrewjpage/master Build for trusty | 14 August 2014, 14:35:45 UTC |
| 4d56e0e | andrewjpage | 14 August 2014, 14:33:14 UTC | Merge branch 'master' of github.com:andrewjpage/gubbins | 14 August 2014, 14:33:14 UTC |
| 6c313b5 | andrewjpage | 14 August 2014, 14:32:59 UTC | update to trusty | 14 August 2014, 14:32:59 UTC |
| 901cd57 | andrewjpage | 14 August 2014, 13:32:13 UTC | build for trusty | 14 August 2014, 13:32:13 UTC |
| 1df26f6 | andrewjpage | 12 August 2014, 15:55:24 UTC | debian changes | 12 August 2014, 15:55:24 UTC |
| 1caef95 | andrewjpage | 12 August 2014, 12:39:40 UTC | Merge pull request #99 from andrewjpage/master Changes from Aidan Delaney | 12 August 2014, 12:39:40 UTC |
| 9a21644 | andrewjpage | 12 August 2014, 12:36:39 UTC | Revert "fix tests" fastml 2 gives slightly different results to fastml3 This reverts commit 0f590c525ed139ff6917d715049c139cc7872aa5. | 12 August 2014, 12:36:39 UTC |
| 0f590c5 | andrewjpage | 12 August 2014, 12:21:53 UTC | fix tests | 12 August 2014, 12:21:53 UTC |
