Re: [R-sig-phylo] Rooting trees in R
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 -- 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
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
Thanks a lot for your prompt response. Best regards De :Jacob Berv A : Valentine Usongo 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 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/
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 > 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/
[R-sig-phylo] Rooting trees in R
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/