Thanks a lot for your prompt response. Best regards
De : Jacob Berv <jakeberv.r.sig.ph...@gmail.com> A : Valentine Usongo <valentine.uso...@inspq.qc.ca> Cc : r-sig-phylo@r-project.org Date : 2017-05-23 13:25 Objet : Re: [R-sig-phylo] Rooting trees in R see root() in the R package ape or reroot() in phytools J > On May 23, 2017, at 1:22 PM, Valentine Usongo <valentine.uso...@inspq.qc.ca> 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/ [[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/
