Prune tree to a list of taxa

Using the {ape} function drop.tip() we can easily excise a single taxon or a list of taxa from our "phylo" tree object in R. However, it is not immediately obvious how to prune the tree to include, rather than exclude, a specific list of tips. Trina Roberts (now at NESCent) shared a trick to do this with me some time ago, and I thought I'd pass it along to the readers of this blog.

First, let's start with a tree of 10 species:

> tree<-rtree(10)
> write.tree(tree)
[1] "(t8:0.22,((((t3:0.9,(t7:0.48,t2:0.5):0.12):0.47,t6:0.55):0.08,(t5:0.49,(t9:0.71,t10:0.13):0.15):0.7):0.87,(t1:0.72,t4:0.62):0.55):0.47);"

Now, say we want to keep the species t2, t4, t6, t8, and t10 in our pruned tree, we just put these tip names into a vector:

> species<-c("t2","t4","t6","t8","t10")

[More commonly, this vector will probably come from the row names in our data matrix, or we might read it from a text file.]

We create the pruned tree with one command:

> pruned.tree<-drop.tip(tree,tree$tip.label[-match(species, tree$tip.label)])

Now we have our pruned tree, as desired:

> write.tree(pruned.tree)
[1] "(t8:0.22,(((t2:1.09,t6:0.55):0.08,t10:0.98):0.87,t4:1.17):0.47);"