Re: [R-sig-phylo] Specifying a polytomy at the root with no outgroup

Thanks so much. That’s perfect. I will update my question at https://www.biostars.org/p/294222/ so it is documented somewhere. Cheers Yan On 20 Jan 2018, at 16:08, Emmanuel Paradis wrote: > Hi, > > To get a tree with a basal multichotomy as a rooted tree, you have

Re: [R-sig-phylo] Specifying a polytomy at the root with no outgroup

Hi, To get a tree with a basal multichotomy as a rooted tree, you have to set its root edge: R> tr <- read.tree(text = "(A,B,(C,D));") R> is.rooted(tr) [1] FALSE R> tr$root.edge <- 0 R> is.rooted(tr) [1] TRUE This could be done directly in the Newick string: R> tr <- read.tree(text =

[R-sig-phylo] Specifying a polytomy at the root with no outgroup

Hi I have a set of rooted trees, some of which have polytomies at the root, like (A,B,(C,D)); ((A,B),(C,D)); These are not treated as rooted by default, so I have tried to root them using root(tree, node = Ntip(phy) + 1, resolve.root = TRUE), but this gives an error, explained here: