tag:blogger.com,1999:blog-749730248446670689.post60112218661320203..comments2024-01-31T19:34:07.460+08:00Comments on The Cabbages of Doom: How to root a phylogenetic treeRichard Edwardshttp://www.blogger.com/profile/16115218690707131186noreply@blogger.comBlogger8125tag:blogger.com,1999:blog-749730248446670689.post-57347828266091036092020-02-29T23:28:50.818+08:002020-02-29T23:28:50.818+08:00Excellent explanation and illustration. Answered m...Excellent explanation and illustration. Answered my questions on how to appropriately interpret a phylogeny tree. Thanks!Anonymoushttps://www.blogger.com/profile/06507951949264164114noreply@blogger.comtag:blogger.com,1999:blog-749730248446670689.post-257607824454541482017-02-22T01:13:20.465+08:002017-02-22T01:13:20.465+08:00Very goodVery goodJilguerohttps://www.blogger.com/profile/03394251839100540927noreply@blogger.comtag:blogger.com,1999:blog-749730248446670689.post-69513227074145266472016-04-11T17:05:29.690+08:002016-04-11T17:05:29.690+08:00You can do. If your phylogenetic inference method ...You can do. If your phylogenetic inference method does not correctly handle rate variation, or it is too extreme, you will still have problems getting the right tree and the outgroup might be stuck in the wrong place. You can get a sense of this by looking at the bootstrap or likelihood values of the two descendant branches where the outgroup joins the rest of the tree. A particular problem is where you have very divergent taxa where the time between divergence was very small relative to the time since divergence; there is little signal to correctly resolve the branching order.Richard Edwardshttps://www.blogger.com/profile/16115218690707131186noreply@blogger.comtag:blogger.com,1999:blog-749730248446670689.post-28553897164667230942016-04-03T20:20:29.580+08:002016-04-03T20:20:29.580+08:00Hi there,
With out-group rooting don't you ha...Hi there,<br /><br />With out-group rooting don't you have the same confounding problem of differing evolutionary rates as you would with mid-point rooting?<br /><br />Cheers,<br /><br />JamesAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-749730248446670689.post-40703622815940502462016-03-13T07:31:59.370+08:002016-03-13T07:31:59.370+08:00If you don't have any way of determining what ...If you don't have any way of determining what the outgroup should be then you cannot use outgroup rooting. If the tree is looking well-behaved, with a fairly constant rate of evolution and reasonably long ancestral branches, you can use midpoint rooting. Otherwise, it is probably safest to leave your tree unrooted. You should always work within the limits and uncertainties of your data - it is much better to say "I don't know", or "there is insufficient signal in the data to determine", than to force the issue.Richard Edwardshttps://www.blogger.com/profile/16115218690707131186noreply@blogger.comtag:blogger.com,1999:blog-749730248446670689.post-84796508782577049432016-03-13T06:14:41.137+08:002016-03-13T06:14:41.137+08:00Thanks so much! But i am still in trouble when you...Thanks so much! But i am still in trouble when you do outgroup rooting. If you don't know whether kangaroo is far different and this is even unknown, what should i doAnonymoushttps://www.blogger.com/profile/06042554842387994148noreply@blogger.comtag:blogger.com,1999:blog-749730248446670689.post-90300518079971269292014-05-28T13:26:09.766+08:002014-05-28T13:26:09.766+08:00Well explained!!ThanksWell explained!!ThanksAnonymoushttps://www.blogger.com/profile/09118623238344162591noreply@blogger.comtag:blogger.com,1999:blog-749730248446670689.post-58612908362446762472013-03-21T18:44:36.209+08:002013-03-21T18:44:36.209+08:00Thanks, i found this very useful. I have been deba...Thanks, i found this very useful. I have been debating how important it is to root a tree when looking at phylogenetics of MLST sequences. I had composed phylogenetics on both unrooted and outgroups methods. Now that i have read this, i will be using the outgroups method so that i can put the ancestry of the different groups into perspective.Anonymoushttps://www.blogger.com/profile/15894696955914894795noreply@blogger.com