| 83721cd | kistlerk | 08 January 2021, 20:06:28 UTC | reorganize manuscript folder | 08 January 2021, 20:06:28 UTC |
| c7945a1 | kistlerk | 08 January 2021, 19:54:35 UTC | final revisions | 08 January 2021, 19:54:35 UTC |
| 21a5db3 | kistlerk | 08 January 2021, 18:53:08 UTC | add reviewer responses | 08 January 2021, 18:53:08 UTC |
| e7d6739 | kistlerk | 08 January 2021, 18:51:00 UTC | final reviewer comments | 08 January 2021, 18:51:00 UTC |
| a45b6e7 | kistlerk | 08 January 2021, 06:40:42 UTC | minor text updates | 08 January 2021, 06:40:42 UTC |
| 702e2c3 | kistlerk | 01 January 2021, 18:33:49 UTC | address pos sel vs adaptive evo | 01 January 2021, 18:33:49 UTC |
| 77af795 | kistlerk | 31 December 2020, 19:02:47 UTC | address reviewer comments relating to TMRCA | 31 December 2020, 19:02:47 UTC |
| 93b55cf | kistlerk | 30 December 2020, 00:14:25 UTC | text about NTD antibodies | 30 December 2020, 00:14:25 UTC |
| 605ec70 | kistlerk | 29 December 2020, 23:57:37 UTC | add rbd to fig 3 | 29 December 2020, 23:57:37 UTC |
| 7ad693c | kistlerk | 29 December 2020, 23:25:48 UTC | add fig 7 supp 2 and more reviewer text | 29 December 2020, 23:25:48 UTC |
| 2c367b8 | kistlerk | 29 December 2020, 17:21:28 UTC | fig 7 supplement | 29 December 2020, 17:21:28 UTC |
| 0cef8b7 | kistlerk | 29 December 2020, 03:07:01 UTC | 10 simulations for fig 7 | 29 December 2020, 03:07:01 UTC |
| 951238b | kistlerk | 29 December 2020, 00:49:50 UTC | update fig 3 and 4 | 29 December 2020, 00:49:50 UTC |
| 9823e05 | kistlerk | 24 December 2020, 18:05:09 UTC | address more reviewer comments | 24 December 2020, 18:05:09 UTC |
| 38ee569 | kistlerk | 22 December 2020, 02:12:20 UTC | minor revisions to manuscript text | 22 December 2020, 02:12:20 UTC |
| 5cd61d3 | kistlerk | 21 December 2020, 21:37:01 UTC | add text about linear increase in adaptive subs. and more revisions | 21 December 2020, 21:37:01 UTC |
| 0229d62 | kistlerk | 19 December 2020, 22:08:12 UTC | Delete ~$vised-Seasonal CoV Adaptive Evolution Manuscript.docx | 19 December 2020, 22:08:12 UTC |
| 13d3aa9 | kistlerk | 19 December 2020, 22:06:57 UTC | dn/ds results added to manuscript | 19 December 2020, 22:06:57 UTC |
| 2f1e8ff | kistlerk | 19 December 2020, 20:15:31 UTC | add paperpile to word doc | 19 December 2020, 20:15:31 UTC |
| 6516cf5 | kistlerk | 19 December 2020, 19:54:06 UTC | Update gitignore | 19 December 2020, 19:54:06 UTC |
| 6722505 | kistlerk | 19 December 2020, 19:53:05 UTC | rename revised manuscript | 19 December 2020, 19:53:05 UTC |
| eaae18f | kistlerk | 19 December 2020, 19:52:01 UTC | Update gitignore for word files | 19 December 2020, 19:52:01 UTC |
| 5228fdc | kistlerk | 19 December 2020, 19:48:13 UTC | first revisions and new figure colors | 19 December 2020, 19:48:13 UTC |
| 5d46116 | kistlerk | 18 December 2020, 21:15:17 UTC | tidy and add function descriptions | 18 December 2020, 21:15:17 UTC |
| df684d8 | kistlerk | 16 December 2020, 16:45:43 UTC | adaptation rates in other genes (like nucleocapsid, envelope) | 16 December 2020, 16:45:43 UTC |
| 569f3b8 | kistlerk | 16 December 2020, 16:43:55 UTC | Update gitignore | 16 December 2020, 16:43:55 UTC |
| 944ee7f | kistlerk | 12 December 2020, 16:22:50 UTC | elife reviewer comments | 12 December 2020, 16:22:50 UTC |
| 07dbd29 | kistlerk | 02 December 2020, 21:01:59 UTC | add directory to run oc43 lineages separately | 02 December 2020, 21:01:59 UTC |
| 5817ad2 | kistlerk | 04 November 2020, 17:55:28 UTC | include manuscript pdfs | 04 November 2020, 17:55:28 UTC |
| a052cf0 | kistlerk | 30 October 2020, 17:18:22 UTC | beast runs and weighted divergence calculations | 30 October 2020, 17:18:22 UTC |
| 66a9780 | kistlerk | 26 October 2020, 20:17:05 UTC | update fig1supp2 and abstract | 26 October 2020, 20:17:05 UTC |
| 5f2a89e | kistlerk | 22 October 2020, 16:15:20 UTC | copy all pact files from local pact repo to this repo | 22 October 2020, 16:15:20 UTC |
| 49c5883 | kistlerk | 22 October 2020, 16:13:55 UTC | add pact files | 22 October 2020, 16:13:55 UTC |
| 50a638d | kistlerk | 22 October 2020, 16:12:06 UTC | new hku1 rooting | 22 October 2020, 16:12:06 UTC |
| a8f6c74 | kistlerk | 13 October 2020, 19:21:30 UTC | fix default auspice coloring | 13 October 2020, 19:21:30 UTC |
| ccef02c | kistlerk | 13 October 2020, 19:19:37 UTC | fix auspice default coloring | 13 October 2020, 19:19:37 UTC |
| 5cbe7ac | kistlerk | 13 October 2020, 19:11:58 UTC | change default auspice coloring to date | 13 October 2020, 19:11:58 UTC |
| b5b38c1 | kistlerk | 13 October 2020, 18:58:37 UTC | fix auspice json names | 13 October 2020, 18:58:37 UTC |
| a258996 | kistlerk | 13 October 2020, 18:02:27 UTC | fix oc43 spike tree for community view | 13 October 2020, 18:02:27 UTC |
| b6dea75 | kistlerk | 13 October 2020, 15:58:25 UTC | update figure numbering | 13 October 2020, 15:58:25 UTC |
| e653aad | kistlerk | 09 October 2020, 21:37:39 UTC | update supps with data from new nl63 trees | 09 October 2020, 21:37:39 UTC |
| 127e720 | kistlerk | 07 October 2020, 16:13:58 UTC | re-rooted nl63 on outgroup | 07 October 2020, 16:13:58 UTC |
| 2f4cb07 | kistlerk | 30 September 2020, 23:56:00 UTC | plot excluding different amounts of simulated data | 30 September 2020, 23:56:00 UTC |
| 43c80ca | kistlerk | 26 September 2020, 01:34:17 UTC | remove gitignore files | 26 September 2020, 01:34:17 UTC |
| 5b4737e | kistlerk | 26 September 2020, 01:30:47 UTC | remove gitignroe files | 26 September 2020, 01:30:47 UTC |
| e14799f | kistlerk | 26 September 2020, 01:18:46 UTC | fix markdown format | 26 September 2020, 01:18:46 UTC |
| 4610be9 | kistlerk | 26 September 2020, 01:16:56 UTC | add readmes | 26 September 2020, 01:16:56 UTC |
| a96d6ed | kistlerk | 26 September 2020, 00:34:20 UTC | change tree json names for community | 26 September 2020, 00:34:20 UTC |
| cc19cb0 | kistlerk | 26 September 2020, 00:25:39 UTC | move jsons for nextstrain/community | 26 September 2020, 00:25:39 UTC |
| 2d970bd | kistlerk | 26 September 2020, 00:16:38 UTC | add gitignore and reorganize repo | 26 September 2020, 00:16:38 UTC |
| 923eddc | kistlerk | 17 September 2020, 17:51:23 UTC | new s1 boundaries | 17 September 2020, 17:51:23 UTC |
| d282824 | kistlerk | 11 September 2020, 21:56:55 UTC | updated clade definitions and redone figures | 11 September 2020, 21:56:55 UTC |
| fdad4f3 | kistlerk | 02 September 2020, 20:01:43 UTC | rdrp references, data and augur run for all covs | 02 September 2020, 20:01:43 UTC |
| a0ec6cd | kistlerk | 24 August 2020, 17:46:28 UTC | fix aaa_muts augur output, plot muts per site | 24 August 2020, 17:46:28 UTC |
| 3747020 | kistlerk | 10 August 2020, 17:45:25 UTC | clean simulation directories and improve plots | 10 August 2020, 17:45:25 UTC |
| 2b8f5d6 | kistlerk | 06 August 2020, 01:48:23 UTC | bhatt analysis on simulated oc43a data | 06 August 2020, 01:48:23 UTC |
| 9ea8ff8 | kistlerk | 05 August 2020, 17:32:01 UTC | bhatt analysis for simualted data | 05 August 2020, 17:32:01 UTC |
| 21dfa3d | kistlerk | 01 August 2020, 20:29:40 UTC | add rdrp to oc43 and update oc43 clade definitions | 01 August 2020, 20:29:40 UTC |
| b805f54 | kistlerk | 20 July 2020, 19:04:33 UTC | testing | 20 July 2020, 19:04:33 UTC |
| 3010a76 | kistlerk | 20 July 2020, 19:02:36 UTC | testing | 20 July 2020, 19:02:36 UTC |
| ee6967f | kistlerk | 20 July 2020, 19:00:54 UTC | testing | 20 July 2020, 19:00:54 UTC |
| 05b1529 | kistlerk | 20 July 2020, 18:56:46 UTC | testing | 20 July 2020, 18:56:46 UTC |
| c141123 | kistlerk | 20 July 2020, 18:47:10 UTC | emperical data viewable next to simulations | 20 July 2020, 18:47:10 UTC |
| f76bd6d | kistlerk | 17 July 2020, 18:32:11 UTC | santa-sim_oc43a-spike runs santa-sim and plots results with auspice Former-commit-id: c73c76d10fdb6d0ee18b2efb908429bba7522134 | 17 July 2020, 18:32:11 UTC |
| a4a76f6 | kistlerk | 01 July 2020, 19:26:39 UTC | tmrca notebooks Former-commit-id: 03984c15bfa7907a11706c4f0a14d9e5d2c4c79b | 01 July 2020, 19:26:39 UTC |
| 78221d6 | kistlerk | 30 June 2020, 16:13:41 UTC | updated clade/lineage plots Former-commit-id: fe61ad3001b33a2cf2d71a9f7af09ed6110d4fb5 | 30 June 2020, 16:13:41 UTC |
| 53608cf | kistlerk | 10 June 2020, 22:47:04 UTC | compare cov to measles and h3n2. and bootstrapping Former-commit-id: 56a9606c2ee4f5003e43aeb4e70d59d0edba8761 | 10 June 2020, 22:47:04 UTC |
| 2332e8e | kistlerk | 26 May 2020, 00:03:00 UTC | separate oc43 and nl63 clades Former-commit-id: 09b0bab2eb035f587bce3a45e95ae4ff187dd6cc | 26 May 2020, 00:03:00 UTC |
| bbba1b7 | kistlerk | 02 May 2020, 23:02:07 UTC | replace all fasta manipulation notebooks with postdownload_formatting notebook Former-commit-id: 9a632a83af97b1fa9397e1b46570b6ccfe3b9fda | 02 May 2020, 23:02:07 UTC |
| 17bf071 | kistlerk | 25 April 2020, 21:05:40 UTC | s1 s2 divergence plots Former-commit-id: e2d7f0648cdd9f8d8058f774702fb976e6dd9e36 | 25 April 2020, 21:05:40 UTC |
| 1d14fa8 | kistlerk | 25 April 2020, 20:54:31 UTC | s1 versus s2 separation and analysis Former-commit-id: 1be51c52d559ff0e6f0ae6da8f106c20cec3d6df | 25 April 2020, 20:54:31 UTC |
| 39f10c6 | kistlerk | 21 April 2020, 21:13:22 UTC | tree from all sequence data Former-commit-id: bdab45c189152b017c94e5ac686497abde7efe80 | 21 April 2020, 21:13:22 UTC |
| 27a97ad | kistlerk | 19 April 2020, 00:25:20 UTC | snakefile exports root seq. Also divergence plots | 19 April 2020, 00:25:20 UTC |
| 0c7b297 | kistlerk | 16 April 2020, 15:27:11 UTC | completed builds for all genes, all viruses | 16 April 2020, 15:27:11 UTC |
| 87d2b70 | kistlerk | 15 April 2020, 19:10:00 UTC | restructure to one repo per virus. Make reference files for each gene | 15 April 2020, 19:10:00 UTC |
| a48f14a | kistlerk | 13 April 2020, 23:11:43 UTC | first stab at bhatt method | 13 April 2020, 23:11:43 UTC |
| 1fb8d85 | kistlerk | 26 March 2020, 23:06:02 UTC | remove country inference | 26 March 2020, 23:06:02 UTC |
| 846d3bf | kistlerk | 24 March 2020, 23:08:04 UTC | initial build set-up | 24 March 2020, 23:08:04 UTC |
