Steps 6 and 7 here relied on us knowing which nodes in the tree to manipulate. This isn't always obvious as the nodes are identified by number and not name. We can get at the node number we want if we use the MRCA() (Most Recent Common Ancestor) function. Simply pass it a vector of node names and it returns the ID of the node that represents the MRCA:

MRCA(itol, tip=c("Photorhabdus_luminescens", "Blochmannia_floridanus"))

This will give the following output:

## 206