{"action":"created","issue":{"url":"https://api.github.com/repos/nextstrain/augur/issues/140","repository_url":"https://api.github.com/repos/nextstrain/augur","labels_url":"https://api.github.com/repos/nextstrain/augur/issues/140/labels{/name}","comments_url":"https://api.github.com/repos/nextstrain/augur/issues/140/comments","events_url":"https://api.github.com/repos/nextstrain/augur/issues/140/events","html_url":"https://github.com/nextstrain/augur/issues/140","id":336736580,"node_id":"MDU6SXNzdWUzMzY3MzY1ODA=","number":140,"title":"augur tree vs augur unrooted","user":{"login":"trvrb","id":1176109,"node_id":"MDQ6VXNlcjExNzYxMDk=","avatar_url":"https://avatars2.githubusercontent.com/u/1176109?v=4","gravatar_id":"","url":"https://api.github.com/users/trvrb","html_url":"https://github.com/trvrb","followers_url":"https://api.github.com/users/trvrb/followers","following_url":"https://api.github.com/users/trvrb/following{/other_user}","gists_url":"https://api.github.com/users/trvrb/gists{/gist_id}","starred_url":"https://api.github.com/users/trvrb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/trvrb/subscriptions","organizations_url":"https://api.github.com/users/trvrb/orgs","repos_url":"https://api.github.com/users/trvrb/repos","events_url":"https://api.github.com/users/trvrb/events{/privacy}","received_events_url":"https://api.github.com/users/trvrb/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-06-28T18:45:09Z","updated_at":"2018-06-29T05:47:11Z","closed_at":"2018-06-29T05:47:11Z","author_association":"MEMBER","body":"Related to #133, but separate enough that I wanted a separate issue.\r\n\r\nSome of my semantic confusion lies in `augur tree`. I think it could be easier for people to immediately understand what's happening if we renamed this to `augur unrooted`. In the Snakefile it would produce `tree_unrooted.nwk` instead of `tree_raw.nwk`.\r\n\r\nI think this flags things more appropriately to say that this tree is not yet rooted. And then we can make it clear that the tree produced by `augur treetime` has been rooted. This should make the change in topology between `tree_raw.nwk` and `tree.nwk` less of a surprise."},"comment":{"url":"https://api.github.com/repos/nextstrain/augur/issues/comments/401254138","html_url":"https://github.com/nextstrain/augur/issues/140#issuecomment-401254138","issue_url":"https://api.github.com/repos/nextstrain/augur/issues/140","id":401254138,"node_id":"MDEyOklzc3VlQ29tbWVudDQwMTI1NDEzOA==","user":{"login":"trvrb","id":1176109,"node_id":"MDQ6VXNlcjExNzYxMDk=","avatar_url":"https://avatars2.githubusercontent.com/u/1176109?v=4","gravatar_id":"","url":"https://api.github.com/users/trvrb","html_url":"https://github.com/trvrb","followers_url":"https://api.github.com/users/trvrb/followers","following_url":"https://api.github.com/users/trvrb/following{/other_user}","gists_url":"https://api.github.com/users/trvrb/gists{/gist_id}","starred_url":"https://api.github.com/users/trvrb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/trvrb/subscriptions","organizations_url":"https://api.github.com/users/trvrb/orgs","repos_url":"https://api.github.com/users/trvrb/repos","events_url":"https://api.github.com/users/trvrb/events{/privacy}","received_events_url":"https://api.github.com/users/trvrb/received_events","type":"User","site_admin":false},"created_at":"2018-06-29T05:47:11Z","updated_at":"2018-06-29T05:47:11Z","author_association":"MEMBER","body":"Closing in favor of suggestion in #133 of `augur tree` + `augur refine`."}}
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