I am very glad that ggtree is now available via Bioconductor. This is my 6th Bioconductor package. ggtree now supports parsing output files from BEAST, PAML, HYPHY, EPA and PPLACER and can annotate phylogenetic tree directly using plot methods.

Now you can use the following command to install ggtree:

install.packages("ggtree",
                 repos = "http://www.bioconductor.org/packages/devel/bioc",
                 type  = "source")

Find out more at http://www.bioconductor.org/packages/3.1/bioc/html/ggtree.html and check out the vignette, http://www.bioconductor.org/packages/3.1/bioc/vignettes/ggtree/inst/doc/ggtree.html

Citation

G Yu, DK Smith, H Zhu, Y Guan, TTY Lam*. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution. doi:10.1111/2041-210X.12628.