My phytools R package gets quite a lot of use. At the time of writing (according to Google Scholar), the paper describing phytools has been cited an astonishing 5,433 times!
Still, many functions of the package get more use than others! I think perhaps the most popular are
(for stochastic mapping),
contMap (for graphing),
fitPagel (for Pagel's
1994 binary character correlation method), and
phylosig (for measuring
Exactly no one asked, but maybe my favorite under-utilized phytools function is the fun (IMO)
Here's a quick reminder of how it works.
##  '1.0.1'
data(mammal.tree) mammal.tree<-ladderize(mammal.tree) data(mammal.data) lnMass<-setNames(log(mammal.data$bodyMass), rownames(mammal.data)) bodyMass.map<-edge.widthMap(mammal.tree,lnMass) plot(bodyMass.map,border="black",color="goldenrod", legend="log(body mass)")