I just submitted a new version of "phytools" to CRAN and it is now available online (phytools CRAN page here). This new version (v0.1-0) has a number of new functions over the previous CRAN version (v0.0-8) but little in terms of functional updates from the last version of "phytools" v0.0-9 which I posted on my website but not to CRAN. Most of the updates in the latest version involve improving the documentation (although there is still a lot of work to be done in this area); removing strictly internally used functions from the namespace (this means they can no longer be accessed by users, which is good); and moving a number of little-used dependencies from "Depends" to "Imports." This helps avoid cluttering the namespace (that is, having too many packages loaded with all their named functions stored in memory).
Note that at time of writing, the Windows & Mac OS versions of "phytools" were still migrating through cyberspace to all the mirror CRAN repositories. Thus, to download the latest version of "phytools" in binary form, please check the list of CRAN mirrors to find one that has the binary versions uploaded (e.g., Austria; please note that in general it is a good idea to pick a CRAN mirror geographically near to you so as to minimize network load).
Comments, problems welcome.