Re: [R-sig-phylo] Rooting trees in R

[Valentine Usongo]

Thanks.



De :Juan Antonio Balbuena <j.a.balbu...@uv.es>
A : valentine.uso...@inspq.qc.ca
Cc :"r-sig-phylo@r-project.org" <r-sig-phylo@r-project.org>
Date :  2017-05-24 04:51
Objet : Re: [R-sig-phylo] Rooting trees in R



As a general reference text to handle phylogentic data and sequences in R, 
you may have a look at
Paradis (2011) Analysis of Phylogenetics and Evolution in R, 2nd edition. 
Springer.

Best wishes

Juan A. Balbuena 


-- 
Dr. Juan A. Balbuena 
Cavanilles Institute of Biodiversity and Evolutionary Biology 
University of Valencia
http://www.uv.es/~balbuena 
P.O. Box 22085
http://www.uv.es/cophylpaco
46071 Valencia, Spain 
e-mail: j.a.balbu...@uv.estel. +34 963 543 658fax +34 963 543 733 
 
NOTE! For shipments by EXPRESS COURIER use the following street address: 
C/ Catedr�tico Jos� Beltr�n 2, 46980 Paterna (Valencia), Spain. 



Libre de virus. www.avast.com 



[[alternative HTML version deleted]]

___
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/

Re: [R-sig-phylo] Rooting trees in R

[Juan Antonio Balbuena]

  
  
As a general reference text to handle phylogentic data and sequences
in R, you may have a look at
Paradis (2011) Analysis of Phylogenetics and Evolution in R, 2nd
edition. Springer.

Best wishes

Juan A. Balbuena 


-- 
  
  

  Dr.
Juan
A. Balbuena 
Cavanilles Institute of Biodiversity and Evolutionary
Biology 
University of
Valencia           
           
           
        http://www.uv.es/~balbuena

P.O. Box
22085           
           
           
           
    http://www.uv.es/cophylpaco
46071 Valencia,
Spain

e-mail: j.a.balbu...@uv.es   
tel.
+34 963 543 658    fax +34 963 543 733 
 
NOTE! For shipments by EXPRESS COURIER use
  the following street
  address: 
  C/ Catedrático José Beltrán 2, 46980 Paterna (Valencia),
  Spain. 
  
  

   
	
  
		Libre de virus. www.avast.com 		
	

 


___
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/

Re: [R-sig-phylo] Rooting trees in R

[Jacob Berv]

see root() in the R package ape or reroot() in phytools
J

> On May 23, 2017, at 1:22 PM, Valentine Usongo  
> wrote:
> 
> Dear members
> 
> My name is Valentine Usongo and  I am a postdoctoral trainee at the INSPQ 
> Montreal-Quebec. I am working on the use of whole genome sequenced based 
> methods for the detection of foodborne outbreaks in Salmonella. I am still 
> a neophyte in the field of bioinformatics. I just concatenated 14 
> individual trees with the cat function in linux. These trees were in 
> newick format and they were generated using the SNVPhyl pipeline 
> of the National Reference Microbiology Laboratory of Canada. These trees 
> were generated by mapping my Salmonella isolates to a reference genome and 
> the only thing that differs in all the trees is the reference genome since 
> each tree has a different reference and my objective here was to assess 
> the impact of the choice of  reference genome on the ability of the SNV 
> method to separate outbreak from nonoutbreak isolates. My  goal is to 
> compare the topologies of these trees using the Kendall-Colijn (rooted) 
> method. This method requires that trees should be rooted but mine are not 
> rooted. 
> Is it possible to root unrooted trees in R or linux and if so how can one 
> go about it ? The metric requires that the input trees should be in the 
> nexus format and they should be rooted. My trees are in newick format and 
> I converted them to nexus in R but then got stuck because I cannot figure 
> how to root the trees. I would be very grateful for your input. 
> Looking forward to hearing from you. 
> Yours sincerely 
> Valentine Usongo 
>   [[alternative HTML version deleted]]
> 
> ___
> 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/

___
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/