| 5f9c17e | andrewjpage | 16 April 2015, 14:33:56 UTC | Merge pull request #138 from andrewjpage/recalculate_genome_length version 1.3.1 | 16 April 2015, 14:33:56 UTC |
| b5b73f6 | andrewjpage | 16 April 2015, 14:32:03 UTC | Merge pull request #137 from andrewjpage/recalculate_genome_length Recalculate genome length | 16 April 2015, 14:32:03 UTC |
| 4e83bb8 | andrewjpage | 16 April 2015, 14:11:37 UTC | version 1.3.1 | 16 April 2015, 14:11:37 UTC |
| ec5904e | andrewjpage | 16 April 2015, 14:09:25 UTC | output genome length minus gaps and recomb as separate stat | 16 April 2015, 14:09:25 UTC |
| 81368c3 | andrewjpage | 14 April 2015, 15:41:12 UTC | calculate genome length for branch as excluding parent recombinations | 14 April 2015, 15:41:12 UTC |
| d7f49b6 | andrewjpage | 14 April 2015, 13:17:24 UTC | Merge pull request #136 from andrewjpage/downstream_recombinations Downstream recombinations | 14 April 2015, 13:17:24 UTC |
| f905435 | andrewjpage | 14 April 2015, 13:14:26 UTC | check input values for window size | 14 April 2015, 13:14:26 UTC |
| 9914f1e | andrewjpage | 14 April 2015, 13:06:50 UTC | allow window size to be set in python | 14 April 2015, 13:06:50 UTC |
| 6eecfa3 | andrewjpage | 14 April 2015, 12:37:06 UTC | pass window max and min in | 14 April 2015, 12:37:06 UTC |
| 1cf5c80 | andrewjpage | 13 April 2015, 14:28:24 UTC | revert to per branch | 13 April 2015, 14:28:24 UTC |
| 16eafeb | andrewjpage | 13 April 2015, 14:05:07 UTC | number of blocks includes all parents | 13 April 2015, 14:05:07 UTC |
| 9967faf | andrewjpage | 13 April 2015, 13:41:22 UTC | update number of snps stats | 13 April 2015, 13:41:22 UTC |
| ed3551f | andrewjpage | 13 April 2015, 13:19:09 UTC | version 1.3.0 | 13 April 2015, 13:19:09 UTC |
| 2ad5336 | andrewjpage | 13 April 2015, 13:15:24 UTC | convert from coords to index in single block test | 13 April 2015, 13:15:24 UTC |
| dd0a537 | andrewjpage | 13 April 2015, 13:05:53 UTC | use merged coords | 13 April 2015, 13:05:53 UTC |
| 03b8935 | andrewjpage | 13 April 2015, 11:04:31 UTC | include the current nodes blocks | 13 April 2015, 11:04:31 UTC |
| 7b7c3af | andrewjpage | 13 April 2015, 10:32:18 UTC | make output array big enough to hold all snps | 13 April 2015, 10:32:18 UTC |
| a20b101 | andrewjpage | 13 April 2015, 10:26:48 UTC | pass through length of snp_locations array | 13 April 2015, 10:26:48 UTC |
| d460593 | andrewjpage | 09 April 2015, 11:11:02 UTC | extra test for a single block | 09 April 2015, 11:11:02 UTC |
| 9482d25 | andrewjpage | 07 April 2015, 10:19:48 UTC | order of indices depends on order of blocks | 07 April 2015, 10:19:48 UTC |
| b99bd75 | andrewjpage | 07 April 2015, 10:15:53 UTC | initialise snp index list | 07 April 2015, 10:15:53 UTC |
| 9ce983d | andrewjpage | 07 April 2015, 10:06:41 UTC | non overlapping block | 07 April 2015, 10:06:41 UTC |
| 0655286 | andrewjpage | 07 April 2015, 10:01:45 UTC | remove debugging | 07 April 2015, 10:01:45 UTC |
| c39864a | andrewjpage | 07 April 2015, 10:01:04 UTC | remove duplicate indices | 07 April 2015, 10:01:04 UTC |
| 0011076 | andrewjpage | 07 April 2015, 09:46:03 UTC | version 1.2.5 | 07 April 2015, 09:46:03 UTC |
| 93f4ec0 | andrewjpage | 07 April 2015, 09:45:03 UTC | block out snps in downstream recombinations | 07 April 2015, 09:45:03 UTC |
| 4d193d8 | andrewjpage | 31 March 2015, 14:02:24 UTC | Merge pull request #135 from andrewjpage/script_version_number output version in python script | 31 March 2015, 14:02:24 UTC |
| f41a877 | andrewjpage | 31 March 2015, 14:01:56 UTC | output version in python script | 31 March 2015, 14:01:56 UTC |
| bdd1854 | andrewjpage | 30 March 2015, 13:59:12 UTC | Merge branch 'master' of github.com:sanger-pathogens/gubbins | 30 March 2015, 13:59:12 UTC |
| 329306d | andrewjpage | 30 March 2015, 13:58:47 UTC | eggs werent included in deb | 30 March 2015, 13:58:47 UTC |
| 15dede9 | andrewjpage | 30 March 2015, 13:18:52 UTC | Merge pull request #134 from andrewjpage/master include last element of array | 30 March 2015, 13:18:52 UTC |
| 6ec565c | andrewjpage | 30 March 2015, 13:18:11 UTC | include last element of array | 30 March 2015, 13:18:11 UTC |
| 7b597ff | andrewjpage | 30 March 2015, 10:37:55 UTC | Merge pull request #133 from andrewjpage/correct_vcf_format Correct vcf format and EMBL format | 30 March 2015, 10:37:55 UTC |
| c10301f | andrewjpage | 30 March 2015, 10:36:52 UTC | update version | 30 March 2015, 10:36:52 UTC |
| 3b68a20 | andrewjpage | 30 March 2015, 10:35:06 UTC | add quotes to tab files test | 30 March 2015, 10:35:06 UTC |
| c8955e2 | andrewjpage | 30 March 2015, 10:27:44 UTC | Merge branch 'correct_vcf_format' of github.com:andrewjpage/gubbins into correct_vcf_format | 30 March 2015, 10:27:44 UTC |
| 8e4bb9c | andrewjpage | 30 March 2015, 10:26:16 UTC | quote out digits in embl format | 30 March 2015, 10:26:16 UTC |
| f6d28f6 | andrewjpage | 30 March 2015, 10:23:49 UTC | corrected vcf test output | 30 March 2015, 10:23:49 UTC |
| edc31b2 | andrewjpage | 30 March 2015, 10:12:49 UTC | pass length of genome through | 30 March 2015, 10:12:49 UTC |
| 6ae3471 | andrewjpage | 30 March 2015, 10:10:17 UTC | add contig line and remove trailing tab | 30 March 2015, 10:10:17 UTC |
| dbe580a | andrewjpage | 30 March 2015, 09:17:27 UTC | Merge pull request #132 from andrewjpage/gap_filling debian changelog | 30 March 2015, 09:17:27 UTC |
| cfd26de | andrewjpage | 30 March 2015, 09:17:01 UTC | debian changelog | 30 March 2015, 09:17:01 UTC |
| fc84f9e | andrewjpage | 30 March 2015, 09:13:58 UTC | Merge pull request #131 from andrewjpage/gap_filling Dont fill in gaps in parent with bases from child | 30 March 2015, 09:13:58 UTC |
| 061e2b8 | andrewjpage | 30 March 2015, 09:06:55 UTC | Dont fill in gaps in parent with bases from child | 30 March 2015, 09:06:55 UTC |
| 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 |
