phangorn is a package for R. To use it, you first need to download and install R. RStudio provides a nice user interface for R.

You can install the latest release version from CRAN

install.packages("phangorn")

or install the latest development version using the install_github function in the devtools package from github.

library(devtools)
install_github("KlausVigo/phangorn")

For devtools to work on windows you need addionally to have installed Rtools and on mac you need Xcode to compile some C code. Once these programs are installed you can install phangorn with the commands above.