force bifurcating trees in r

Hi all, I've run into the following problem a few times now (most recently with the species tree program STAR): Some programs require input trees that are strictly bifurcating. In other words, they are not allowed to have any polytomies/multifurcations/multichotomies. 

I wish my trees were always strictly bifurcating! But sometimes that's just not the case.

Here's a simple workaround in R using the package APE. The crucial command is multi2di, which transforms all polytomies into a series of dichotomies with one or more branches of length zero. Here's my R code:

###Code for a Phylo Object###
library(ape)

myTree<-read.tree("myTree.tre")

is.binary.tree(myTree)
[1] FALSE

myTree.bifurcating<-multi2di(myTree)

is.binary.tree(myTree.bifurcating)
[1] TRUE

write.tree(myTree.bifurcating, file="myTree.bifurcating.tre")

###Code for a Multiphylo Object###
library(ape)

myTrees<-read.tree("myTrees.tre")

is.binary.tree(myTrees[[1]])
[1] FALSE

make.bifurcating<-function(phy){
  for(i in 1:length(phy)){
    phy[[i]]<-multi2di(phy[[i]])
  }
  return(phy)
}

myTrees.bifurcating<-make.bifurcating(myTrees)

is.binary.tree(myTrees.bifurcating[[1]])
[1] TRUE

write.tree(myTree.bifurcating, file="myTrees.bifurcating.trees")

NOTE: I would NOT recommend using poorly resolved trees with multiple polytomies as an input into any program that assumes or depends on the accuracy of gene trees. That said, if you have lots of gene trees with just one or two small polytomies, this method works pretty well.