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

[Yan Wong]

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

[Emmanuel Paradis]

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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Pour nous remonter une erreur de filtrage, veuillez vous rendre ici : 
http://f.security-mail.net/304anPlLmqF




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

[Yan Wong]

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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