Dear Brian, Awesome. Thanks for sharing the code Brian. I will give it a try. I see what you all mean now more precisely with the question of what does it really mean to have branch lengths on a consensus tree.
Thanks, Scott On Wed, Nov 21, 2012 at 11:10 AM, Brian O'Meara <bome...@utk.edu> wrote: > > I have a function to create a consensus tree with branch lengths. You feed > it a given topology (often a consensus topology, made with ape), then a > list of trees, and tell it what you want the branch lengths to represent. > It could be the proportion of input trees with that edge (good for > summarizing bootstrap or Bayes proportions) or the mean, median, or sd of > branch lengths for those trees that have that edge. Consensus branch > lengths in units of proportion of matching trees has obvious utility. As > Daniel says, the average branch lengths across a set of trees is more > difficult to see a use case for, but you could imagine doing something like > taking the ratogram output from r8s on a set of trees and summarizing the > rate average and rate sd on a given, "best", tree as two sets of branch > lengths on that tree. > > I've put the function source at > https://r-forge.r-project.org/scm/viewvc.php/*checkout*/pkg/R/consensusBrlen.R?revision=110&root=omearalab. > You can source the file for the function (consensusBrlen() ) and other > functions it needs. It also uses phylobase. Note that this is alpha-quality > code -- it's been checked a bit, but verify it's doing what you want. > > Here's an example of how to use it > > library(ape) > > library(phylobase) > > phy.a<-rcoal(15) > > phy.b<-phy.a > > phy.b$edge.length<-phy.b$edge.length+runif(length(phy.b$edge.length), 0, > 0.1) > > phy.c<-rcoal(15) > > phy.list<-list(phy.a, phy.b, phy.c) > > phy.consensus<-consensusBrlen(phy.a, list(phy.a, phy.b, phy.c), > type="mean_brlen") > > > Best, > Brian > > > PS: Note that I am actively looking for grad students: info at > http://www.brianomeara.info/lab . Guaranteed five years support, subject > to decent performance. > > _______________________________________ > Brian O'Meara > Assistant Professor > Dept. of Ecology & Evolutionary Biology > U. of Tennessee, Knoxville > http://www.brianomeara.info > > Students wanted: Applications due Dec. 15, annually > Postdoc collaborators wanted: Check NIMBioS' website > Calendar: http://www.brianomeara.info/calendars/omeara > > > > On Wed, Nov 21, 2012 at 11:09 AM, Daniel Barker <d...@st-andrews.ac.uk>wrote: > >> Dear Scott, >> >> What should branch lengths on a consensus tree represent? >> >> They cannot be expected substitutions per residue. This would imply no >> evolution at points where uncertain branching patterns have been reduced >> to a multi-furcation - which is not what the multi-furcation is meant to >> imply. (Rather: there was evolution, but we aren't very certain about the >> branching pattern.) >> >> But, MrBayes does provide average lengths of some kind. >> >> Best wishes, >> >> Daniel >> >> On 21/11/2012 15:13, "Scott Chamberlain" <myrmecocys...@gmail.com> wrote: >> >> >When making a consensus tree using ape::consensus the branch lengths are >> >lost. Is there a way to not lose the branch lengths? Or to add them >> >somehow >> >to the consensus tree after making it. >> > >> >library(ape) >> >> >> >> >>cat("owls(((Strix_aluco:4.2,Asio_otus:4.1):4.1,Athene_noctua:7.3):6.3,Tyt >> >>o_alba:13.5);", file = "ex1.tre", sep = "\n")> >> >> >>cat("owls(((Strix_aluco:1.2,Asio_otus:4.5):3.1,Athene_noctua:7.3):6.3,Tyt >> >>o_alba:13.5);", file = "ex2.tre", sep = "\n")> >> >> >>cat("owls(((Strix_aluco:3.2,Asio_otus:4.7):8.1,Athene_noctua:7.3):6.3,Tyt >> >>o_alba:13.5);", file = "ex3.tre", sep = "\n")> tree1 <- >> >>read.tree("ex1.tre")> tree2 <- read.tree("ex2.tre")> tree3 <- >> >>read.tree("ex3.tre")> trees <- c(tree1, tree2, tree3)> trees_con <- >> >>consensus(trees)> trees_con >> >Phylogenetic tree with 4 tips and 3 internal nodes. >> >Tip labels:[1] "Strix_aluco" "Asio_otus" "Athene_noctua" >> "Tyto_alba" >> >Rooted; no branch lengths. >> > >> > >> >Thanks, Scott Chamberlain >> > >> > [[alternative HTML version deleted]] >> > >> >_______________________________________________ >> >R-sig-phylo mailing list >> >R-sig-phylo@r-project.org >> >https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> > >> >> >> -- >> Daniel Barker >> http://bio.st-andrews.ac.uk/staff/db60.htm >> The University of St Andrews is a charity registered in Scotland : No >> SC013532 >> >> _______________________________________________ >> R-sig-phylo mailing list >> R-sig-phylo@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> > > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
