This is in response to a user request to the effect of I would like to place a vertical bar next to all the tips descended for a node that I specify. How do I do this?. Here's my answer:
First, here's our original tree. (Simulated, but generated to look like a realistic empirical tree).
## get the tips numbers & thus their vertical
## we're going to use these later!
## they assume cex=1, but could be adjusted otherwise
## max height of the tips in our clade
## + their labels
## vertical line
## upper & lower horizontal lines to demarcate the
## clade; their specific length is arbitrary
## label for the clade
"clade of interest name",srt=90,pos=1)
That's pretty much it. Of course, the user should adapt this code to their specific tree and visualization goals.