{"action":"created","issue":{"url":"https://api.github.com/repos/trvrb/dynamics-practical/issues/1","repository_url":"https://api.github.com/repos/trvrb/dynamics-practical","labels_url":"https://api.github.com/repos/trvrb/dynamics-practical/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/trvrb/dynamics-practical/issues/1/comments","events_url":"https://api.github.com/repos/trvrb/dynamics-practical/issues/1/events","html_url":"https://github.com/trvrb/dynamics-practical/issues/1","id":142570828,"number":1,"title":"negative branch lengths in skyline tree","user":{"login":"GuangchuangYu","id":626539,"avatar_url":"https://avatars.githubusercontent.com/u/626539?v=3","gravatar_id":"","url":"https://api.github.com/users/GuangchuangYu","html_url":"https://github.com/GuangchuangYu","followers_url":"https://api.github.com/users/GuangchuangYu/followers","following_url":"https://api.github.com/users/GuangchuangYu/following{/other_user}","gists_url":"https://api.github.com/users/GuangchuangYu/gists{/gist_id}","starred_url":"https://api.github.com/users/GuangchuangYu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/GuangchuangYu/subscriptions","organizations_url":"https://api.github.com/users/GuangchuangYu/orgs","repos_url":"https://api.github.com/users/GuangchuangYu/repos","events_url":"https://api.github.com/users/GuangchuangYu/events{/privacy}","received_events_url":"https://api.github.com/users/GuangchuangYu/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2016-03-22T07:29:52Z","updated_at":"2016-03-24T06:32:25Z","closed_at":null,"body":"I find the skyline tree have many (31 in total) negative branch lengths in <http://bedford.io/projects/dynamics-practical/examine-the-skyline-tree.html>\r\n\r\n![](http://bedford.io/projects/dynamics-practical/images/figtree_skyline.png)\r\n\r\nI re-plot this figure using [ggtree](http://www.bioconductor.org/packages/ggtree) and highlight those branches with 'red' color.\r\n\r\n![screenshot 2016-03-22 15 26 48](https://cloud.githubusercontent.com/assets/626539/13944716/93cf56ae-f042-11e5-98c4-970e1960b56c.png)\r\n\r\nThe offspring can't be older than their ancestor.\r\nCan you kindly explain why this happen? \r\n"},"comment":{"url":"https://api.github.com/repos/trvrb/dynamics-practical/issues/comments/200695479","html_url":"https://github.com/trvrb/dynamics-practical/issues/1#issuecomment-200695479","issue_url":"https://api.github.com/repos/trvrb/dynamics-practical/issues/1","id":200695479,"user":{"login":"GuangchuangYu","id":626539,"avatar_url":"https://avatars.githubusercontent.com/u/626539?v=3","gravatar_id":"","url":"https://api.github.com/users/GuangchuangYu","html_url":"https://github.com/GuangchuangYu","followers_url":"https://api.github.com/users/GuangchuangYu/followers","following_url":"https://api.github.com/users/GuangchuangYu/following{/other_user}","gists_url":"https://api.github.com/users/GuangchuangYu/gists{/gist_id}","starred_url":"https://api.github.com/users/GuangchuangYu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/GuangchuangYu/subscriptions","organizations_url":"https://api.github.com/users/GuangchuangYu/orgs","repos_url":"https://api.github.com/users/GuangchuangYu/repos","events_url":"https://api.github.com/users/GuangchuangYu/events{/privacy}","received_events_url":"https://api.github.com/users/GuangchuangYu/received_events","type":"User","site_admin":false},"created_at":"2016-03-24T06:32:25Z","updated_at":"2016-03-24T06:32:25Z","body":"Thank you for clarifying.\r\n\r\nLast question. The output tree has 3 features, rate, height and length. I know rate is clade probability and height are time from node to root. I can't figure out what's the meaning of `length`. Can you explain it or give me some references to study? \r\n\r\nThank you!"}}