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

> 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 
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