tag:blogger.com,1999:blog-8499895524521663926.post663919629318146128..comments2024-03-27T07:13:39.236-04:00Comments on Phylogenetic Tools for Comparative Biology: 'Tangled trees' from add.randomLiam Revellhttp://www.blogger.com/profile/04314686830842384151noreply@blogger.comBlogger4125tag:blogger.com,1999:blog-8499895524521663926.post-62607521326026514122013-02-25T15:59:30.030-05:002013-02-25T15:59:30.030-05:00More on this here. - LiamMore on this <a href="http://blog.phytools.org/2013/02/more-on-untangling-misplotted-trees.html" rel="nofollow">here</a>. - LiamLiam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-17585273266333400332013-02-25T14:13:27.848-05:002013-02-25T14:13:27.848-05:00Thanks Dave.
Cool. Yes, I just wrote a utility fu...Thanks Dave.<br /><br />Cool. Yes, I just wrote a utility function that I'll post shortly in which the user can choose either option.<br /><br />One thing that I discovered, though, is that reorder.phylo(...,"cladewise") does <i>not</i> untangle crossing branches even when reorder(reorder(...,"pruningwise"),"cladewise") does.<br /><br />More later.Liam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-77829018256165850562013-02-25T13:59:14.642-05:002013-02-25T13:59:14.642-05:00I can't remember the exact circumstances, but ...I can't remember the exact circumstances, but I know I've found instances where reorder.phylo wasn't enough and using the read.tree(write.tree()) trick was necessary.dwbapsthttps://www.blogger.com/profile/17606476387441191531noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-42464408476961659352013-02-25T13:14:31.899-05:002013-02-25T13:14:31.899-05:00OK - let me amend my caveat. It seems that for the...OK - let me amend my caveat. It seems that for the reorder.phylo method, the node numbers and the order of tip.label is constant; however for the read.tree(write.tree(...)) method, the order and node numbers can change.Liam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.com