Here's a sample of some of the updates relative to the last major release of phytools:
1. A new version of plotSimmap that uses colors from palette() if none are provided.
5. A new, totally rewritten version of reroot, a function to re-root a tree along any internal or terminal edge.
6. A new function ltt95 to compute the (1-α)% confidence interval around a lineage-through-time plot from a set of trees.
7. A bunch of cool updates to pbtree including: simulating in discrete or continuous-time; simulating with taxa or time stops or both (by two different methods: 1, 2); and simulating deaths as well as births.
8. An updated version of anc.ML, that should work much better for large trees.
9. A new method for conducting marginal ancestral state reconstruction of discrete characters when tip values are uncertain.
It may be a few days before this update is available on CRAN, but interested users can download & install from source from the phytools page. Please let me know of any bugs or issues!