I just posted a new version of phytools, version 0.1-2, to my webpage, here. I have also submitted this version to CRAN (but it will probably take a day or two to be accepted, and then a few days more to percolate through all the mirror repositories). In the meantime, it can be installed in Windows by downloading the file phytools_0.1-2.zip and then typing:
at the prompt. (For instructions on how to install on Mac/Linux/Unix from source, please see my website.)
New features in this version of phytools include:
1) A new function, anc.Bayes(), for Bayesian ancestral state estimation.
2) A new function, vcvPhylo(), to compute the so-called phylogenetic variance covariance matrix including ancestral nodes. I posted about this function here.
Check it out!