{"action":"opened","issue":{"url":"https://api.github.com/repos/glennhickey/progressiveCactus/issues/109","repository_url":"https://api.github.com/repos/glennhickey/progressiveCactus","labels_url":"https://api.github.com/repos/glennhickey/progressiveCactus/issues/109/labels{/name}","comments_url":"https://api.github.com/repos/glennhickey/progressiveCactus/issues/109/comments","events_url":"https://api.github.com/repos/glennhickey/progressiveCactus/issues/109/events","html_url":"https://github.com/glennhickey/progressiveCactus/issues/109","id":323423182,"number":109,"title":"Sensitivity to tree topology and branch lengths?","user":{"login":"jasonsydes","id":182702,"avatar_url":"https://avatars2.githubusercontent.com/u/182702?v=4","gravatar_id":"","url":"https://api.github.com/users/jasonsydes","html_url":"https://github.com/jasonsydes","followers_url":"https://api.github.com/users/jasonsydes/followers","following_url":"https://api.github.com/users/jasonsydes/following{/other_user}","gists_url":"https://api.github.com/users/jasonsydes/gists{/gist_id}","starred_url":"https://api.github.com/users/jasonsydes/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jasonsydes/subscriptions","organizations_url":"https://api.github.com/users/jasonsydes/orgs","repos_url":"https://api.github.com/users/jasonsydes/repos","events_url":"https://api.github.com/users/jasonsydes/events{/privacy}","received_events_url":"https://api.github.com/users/jasonsydes/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-05-15T23:54:30Z","updated_at":"2018-05-15T23:54:30Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"Hello there!\r\n\r\nThe summary: How sensitive is Progressive Cactus to input tree topology and/or branch lengths?  (Mainly in terms of correctness, but we're also curious about runtime...)\r\n\r\nWe're trying to build a tree so that we can begin using Progressive Cactus.  At the moment, we're stuck on the fact that we don't understand how sensitive Cactus is to the tree.  We have certainly seen that [runtime suffers dramatically if you give Cactus a star guide tree](https://github.com/glennhickey/progressiveCactus/issues/73#issuecomment-270775698) (Cactus does much better if you give it a binary guide tree).\r\n\r\nFair enough, we can provide Cactus a binary guide tree.  How carefully do we need to build that tree?  What if we get the topology a little wrong?  A lot wrong?  We've seen [at least some other people are using a tree with no branch lengths](https://github.com/glennhickey/progressiveCactus/issues/87).  Is that best practice?  Or is it better to use a tree with branch lengths?  How sensitive is Cactus to branch lengths?  What if we get the branch lengths a little wrong?  A lot wrong?\r\n\r\nWe're just trying to get a sense of how much effort we should dedicate to this aspect of running Cactus.\r\n\r\nThank you so much for your time!\r\nJason Sydes"}}
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