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. 



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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 		
	

 


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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]]
> 
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[R-sig-phylo] Rooting trees in R

[Valentine Usongo]

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]]

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