Hi,

`To get a tree with a basal multichotomy as a rooted tree, you have to`

`set its root edge:`

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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 = "(A,B,(C,D)):0;") R> is.rooted(tr) [1] TRUE Best, Emmanuel Le 19/01/2018 à 23:08, Yan Wong a écrit :

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: https://www.mail-archive.com/r-sig-phylo@r-project.org/msg03805.html Note that in my case there is no particular reason to specify either A, B, or (C,D) as an outgroup I should explain that what I am trying to do is to calculate distance metrics between these trees (using metrics that are valid with polytomies, such as the KC metric), such that the pairwise distances between (A,B,(C,D)) and (B,A,(C,D)) and ((C,D), B, A) etc are all 0, but the distance between, say, (A,B,(C,D)) and ((A,B),(C,D)) or perhaps (A,C,(B,D)); is not zero. So how can I specify a polytomy at the root, with the tree format used in R? Cheers Yan Wong Oxford _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ Pour nous remonter une erreur de filtrage, veuillez vous rendre ici : http://f.security-mail.net/304anPlLmqF

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