Simulate a tree with an outgroup on a long branch.

simdeepbranch.R

# Code from Liam Revell, and put up here by Scott Chamberlain

require(phytools); require(geiger) # load packages
ntaxa1<-20; ntaxa2<-2 # number of taxa in each clade
total.height<-10 # total tree height (may need to be adjusted)

# simulate subtree 1
tr1<-birthdeath.tree(b=1,d=0,taxa.stop=ntaxa1)
tr1$tip.label<-1:ntaxa1; tr1$root.edge<-0

# simulate subtree 2
tr2<-birthdeath.tree(b=1,d=0,taxa.stop=ntaxa2)
tr2$tip.label<-1:ntaxa2+ntaxa1; tr2$root.edge<-0

# compute tree heights, so that the whole thing can be ultrametric
height1<-max(nodeHeights(tr1))
height2<-max(nodeHeights(tr2))

# create the basal split
tr3<-list(Nnode=1,edge=matrix(c(3,1,3,2),2,2,byrow=T),edge.length=c(total.height-height1,total.height-height2),tip.label=c("tr1","tr2"))
class(tr3)<-"phylo"

# attach the two subtrees one by one
tr3$tip.label[tr3$tip.label=="tr1"]<-"NA"
tr3<-paste.tree(tr3,tr1)
tr3$tip.label[tr3$tip.label=="tr2"]<-"NA"
tr3<-paste.tree(tr3,tr2)

# plot the full tree
plot(tr3)