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 <emmanuel.para...@ird.fr> wrote:

> 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 = "(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
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