Thanks for the suggestions! *Chris Law **|* * *PhD Student *|* * *University of California, Santa Cruz
Coastal Biology Building 130 McAllister Way Santa Cruz, CA 95060 cj...@ucsc.edu *|* research.pbsci.ucsc.edu/eeb/cjlaw/ Small Mammal Research in the Forest Internship <http://research.pbsci.ucsc.edu/envs/smurf> On Thu, Apr 26, 2018 at 3:31 PM, Liam J. Revell <liam.rev...@umb.edu> wrote: > If your case is simple - like you have a tree with tips labeled by > genus, and each species label from each subtree to be bound has tip > labels in the format Genus_species, this could be done using bind.tree > in ape. > > For instance: > > library(phytools) > ## here's your backbone > backbone<-read.tree(text="((A:2.0,B:2.0):1,C:3.0);") > plotTree(backbone) > > ## here are your subtrees > A<-read.tree(text="(A_sp1:1.0,A_sp2:1.0);") > B<-read.tree(text="(B_sp1:1.5,B_sp2:1.5);") > C<-read.tree(text="((C_sp1:0.5,C_sp2:0.5):0.5,C_sp3:1.0);") > subtrees<-c(A,B,C) > > for(i in 1:length(subtrees)){ > genus<-strsplit(subtrees[[i]]$tip.label[[1]],"_")[[1]][1] > h<-max(nodeHeights(subtrees[[i]])) > tip<-which(backbone$tip.label==genus) > backbone$edge.length[which(backbone$edge[,2]==tip)]<- > backbone$edge.length[which(backbone$edge[,2]==tip)]-h > backbone<-bind.tree(backbone,subtrees[[i]],where=tip) > } > > plotTree(backbone) > > Something like that. > > (Of course you could also modify this so that you just manually identify > the tips to bind to. Given the small size of your problem this is probably > what you want.) > > All the best, Liam > > Liam J. Revell, Associate Professor of Biology > University of Massachusetts Boston > & Profesor Asociado, Programa de Biología > Universidad del Rosario > web: http://faculty.umb.edu/liam.revell/ > > On 4/26/2018 4:19 PM, Brian O'Meara wrote: > >> Look at congruify.phylo in geiger (and the associated paper: Eastman >> JM, LJ Harmon, and DC Tank. 2013. Congruification: support for time >> scaling large phylogenetic trees. Methods in Ecology and Evolution). >> >> You could also look into SDM in ape (converting trees [not data] to >> distance matrices, first): relevant paper Criscuolo, A., Berry, V., >> Douzery, E. J. P. , and Gascuel, O. (2006) SDM: A fast >> distance-based approach for (super)tree building in phylogenomics. >> Systematic Biology, 55, 740–755. >> >> Best, Brian >> >> _______________________________________________________________________ >> >> >> Brian O'Meara, http://www.brianomeara.info, especially Calendar > >> <http://brianomeara.info/calendars/omeara/>, CV < >> http://brianomeara.info/cv/>, and Feedback <http://brianomeara.info/teach >> ing/feedback/> >> >> Associate Professor, Dept. of Ecology & Evolutionary Biology, UT >> Knoxville Associate Head, Dept. of Ecology & Evolutionary Biology, UT >> Knoxville Associate Director for Postdoctoral Activities, National >> Institute for Mathematical & Biological Synthesis >> <http://www.nimbios.org> (NIMBioS) >> >> >> On Thu, Apr 26, 2018 at 5:07 PM, Chris Law <cj...@ucsc.edu> wrote: >> >> Hi all, >>> >>> I am trying to graft 3 chronograms onto a family level backbone. >>> Does anybody have any suggestions on what is the best way to do >>> this? Or is going through the tree files in textwrangler the only >>> way to do this. >>> >>> Thanks! >>> >>> >>> *Chris Law **|* * *PhD Student *|* * *University of California, >>> Santa Cruz >>> >>> >>> Coastal Biology Building 130 McAllister Way Santa Cruz, CA 95060 >>> cj...@ucsc.edu *|* research.pbsci.ucsc.edu/eeb/cjlaw/ Small Mammal >>> Research in the Forest Internship <http://research.pbsci.ucsc.ed >>> u/envs/smurf> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ R-sig-phylo mailing >>> list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/l >>> istinfo/r-sig-phylo Searchable >>> archive at http://www.mail-archive.com/r- sig-ph...@r-project.org/ >>> >>> >> [[alternative HTML version deleted]] >> >> _______________________________________________ R-sig-phylo mailing >> list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/l >> istinfo/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/
