Re: [R-sig-phylo] Measures of dissimilarity between phylogenetic trees

[Bruno de Medeiros]

Hi Liam,

Many thanks.

Just an additional question related to Robinson-Foulds distance. It seems
RF.dist() requires the compared trees to be binary. Is there any standard
procedure for dealing with multifurcating trees?

Best,

Bruno
--
Bruno A. S. de Medeiros
PhD Student - Farrell Lab
Harvard University


2011/12/26 Liam J. Revell 

> Hi Bruno.
>
> RF.dist in the phangorn package computes Robinson-Foulds distance (
> http://en.wikipedia.org/wiki/**Robinson-Foulds_metric).
> This is not obvious, but (unless you want the position of the root to
> affect the score) you should probably unroot your trees before using
> RF.dist, e.g.:
> > tr1<-read.tree(text="(A,(B,C))**;")
> > plot(tr1)
> > tr2<-read.tree(text="((A,B),C)**;")
> > # tr1 & tr2 have the same unrooted topology, yet:
> > RF.dist(tr1,tr2)
> [1] 2
> > RF.dist(unroot(tr1),unroot(**tr2))
> [1] 0
>
> In addition, phangorn:treedist and ape:dist.topo provide other metrics of
> tree distance.
>
> All the best, Liam
>
> --
> Liam J. Revell
> University of Massachusetts Boston
> web: 
> http://faculty.umb.edu/liam.**revell/
> email: liam.rev...@umb.edu
> blog: http://phytools.blogspot.com
>
>
> On 12/26/2011 6:27 PM, Bruno de Medeiros wrote:
>
>> Hi everyone,
>>
>> I am simulating characters evolving in a phylogetic tree under a number of
>> models and using those characters to build another tree using parsimony.
>> I would like, then, to measure how similar are the recovered trees when
>> compared to the original ones, taking only topology into account. Is there
>> any function in the R packages to calculate tree distance metrics? I
>> considered using TNT (the program that I am using to build phylogenies) to
>> calculate SPR distances, but it would be much more convenient if there
>> were
>> a way of doing it in R.
>>
>> Thanks in advance,
>>
>> Bruno
>> --
>> Bruno A. S. de Medeiros
>> PhD Student - Farrell Lab
>> Harvard University
>>
>>[[alternative HTML version deleted]]
>>
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>>
>

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Re: [R-sig-phylo] Measures of dissimilarity between phylogenetic trees

[Liam J. Revell]

Hi Bruno.

RF.dist in the phangorn package computes Robinson-Foulds distance 
(http://en.wikipedia.org/wiki/Robinson-Foulds_metric). This is not 
obvious, but (unless you want the position of the root to affect the 
score) you should probably unroot your trees before using RF.dist, e.g.:

> tr1<-read.tree(text="(A,(B,C));")
> plot(tr1)
> tr2<-read.tree(text="((A,B),C);")
> # tr1 & tr2 have the same unrooted topology, yet:
> RF.dist(tr1,tr2)
[1] 2
> RF.dist(unroot(tr1),unroot(tr2))
[1] 0

In addition, phangorn:treedist and ape:dist.topo provide other metrics 
of tree distance.


All the best, Liam

--
Liam J. Revell
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://phytools.blogspot.com

On 12/26/2011 6:27 PM, Bruno de Medeiros wrote:

Hi everyone,

I am simulating characters evolving in a phylogetic tree under a number of
models and using those characters to build another tree using parsimony.
I would like, then, to measure how similar are the recovered trees when
compared to the original ones, taking only topology into account. Is there
any function in the R packages to calculate tree distance metrics? I
considered using TNT (the program that I am using to build phylogenies) to
calculate SPR distances, but it would be much more convenient if there were
a way of doing it in R.

Thanks in advance,

Bruno
--
Bruno A. S. de Medeiros
PhD Student - Farrell Lab
Harvard University

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[R-sig-phylo] Measures of dissimilarity between phylogenetic trees

[Bruno de Medeiros]

Hi everyone,

I am simulating characters evolving in a phylogetic tree under a number of
models and using those characters to build another tree using parsimony.
I would like, then, to measure how similar are the recovered trees when
compared to the original ones, taking only topology into account. Is there
any function in the R packages to calculate tree distance metrics? I
considered using TNT (the program that I am using to build phylogenies) to
calculate SPR distances, but it would be much more convenient if there were
a way of doing it in R.

Thanks in advance,

Bruno
--
Bruno A. S. de Medeiros
PhD Student - Farrell Lab
Harvard University

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