Thank you very much Liam, reroot solved the problem smoothly. Sorry for taking your time with what seemed to be a rookie mistake.
Once again, thank you. Rodrigo Aluizio, Biologist Universidade Federal do Paraná Em sex, 21 de ago de 2015 às 15:08, Liam J. Revell <liam.rev...@umb.edu> escreveu: > Hi Rodrigo. > > resolve.root resolves the root with a branch of zero length - so when > plotted, your tree would still look like it has a basal trichotomy. > There is a function, reroot, in the phytools package that can be used to > re-root the tree along an edge. You can also investigate midpoint.root > in phytools or the faster midpoint in phangorn, which do midpoint > rooting and will usually result in a bifurcation at the root of the tree. > > I hope this is of help. > > All the best, Liam > > Liam J. Revell, Assistant Professor of Biology > University of Massachusetts Boston > web: http://faculty.umb.edu/liam.revell/ > email: liam.rev...@umb.edu > blog: http://blog.phytools.org > > On 8/21/2015 1:55 PM, Rodrigo Aluizio wrote: > > Hi everyone. > > > > I am new to this list as to the use of R for plotting phylogenies, but I > am > > quite used to R in general. Therefore, I am aware of how flexible and > > powerful its graphics “abilities” are. Even so, I am having a very hard > > time trying to root my phylogeny. > > > > I get a MrBayes output (conformat = simple. Yes, already solved this one > - J), > > which seems to be initially unrooted. Then, as the script bellow shows, I > > tried to root it, but unsuccessfully. > > > > > > library(ape) > > > > mytree <- read.nexus("MyTree.tre") > > > > mytree <- unroot(mytree) > > > > mytree <- root(mytree, outgroup = "9", resolve.root = T) > > > > > > > > plot(mytree) > > > > nodelabels(mytree$node.label, adj = c(1.2, -0.5), cex = 0.7, font = 2, > > frame = "n") > > > > add.scale.bar(0.25, 1) > > > > > > > > Searching the web I found this thread: > > https://stat.ethz.ch/pipermail/r-sig-phylo/2015-April/003979.html, but > was > > unable to use it in my favor. I tried multi2di, resolve.root = F, and > =T. I > > tried to root at node, outgroup, both… > > > > The issue is that, every single time I got a trichotomy at the “base” > (some > > errors obviously occurred too) and cannot resolve it. > > > > Any ideas on what am I missing here? > > > > Here are some links that may illustrate the case. > > > > Desired tree -> > > > https://docs.google.com/uc?id=0Bxw4TnKHoFidUnJBSmM0UnJ3Wm8&export=download > > > > Obtained tree -> > > > https://docs.google.com/uc?id=0Bxw4TnKHoFidNjFNMXBKNXF2cG8&export=download > > > > MrBayes output -> > > > https://docs.google.com/uc?id=0Bxw4TnKHoFidQzBBZXNNUEdzTWs&export=download > > > > [[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/
