All furcating trees

Brian O'Meara posted a while ago to R-sig-phylo that he was looking for code to find all bi- and multifurcating rooted trees for a set of taxa. I realized that a function to generate all unrooted trees would be straightforward to program using my add.everywhere() function described previously. [Adding rootedness should then merely involve going through each tree and placing the root along each edge.]

I ran into a few difficulties doing this, one being that the ordering of $edge was somehow incompatible with plot.phylo() for some trees (but I couldn't figure out how). To get around this, I added the option to.plot, which if set to TRUE uses:

trees<-read.tree(text=write.tree(trees))

Unfortunately, my code for this (called allFurcTrees() and available on my R-phylogenetics page, direct link here) runs very slowly. For instance, even with to.plot=FALSE it takes 7 minutes to run for 8 taxa. I have passed the code along to Brian, and hopefully if he intends to use it, he will be able to make it more efficient. I did use the code to create the neat movie (showing all possible bi- and multifurcating trees for 7 taxa), below.



To make your own, just use the following code (or some variant). This code will create a large number (2,752 in this case) .png files, which can then be combined as frames in your movie using a standard movie-making software (for instance, the Windows Live Movie Maker that is free with Windows 7). I'm not sure if there is anyway to generate the animation directly from R.

source("allFurcTrees.R")
trees<-allFurcTrees(n=7,c("A","B","C","D","E","F","G"), to.plot=TRUE)
for(i in 1:length(trees)){
plot(trees[[i]],type="unrooted")
savePlot(file=paste("tree",i,".png",collapse="",sep=""), type="png")
}