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

[Valentine Usongo]

Thanks.



De :Juan Antonio Balbuena 
A : valentine.uso...@inspq.qc.ca
Cc :"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 


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University of Valencia
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