#phylojjeny

#Jack and Jasper's suite of miscellaneous utilities for phylogenetics in R

A collection of helper functions inspired by and largely building on Christoph Heibl's phyloch package (http://www.christophheibl.de/Rpackages.html).

These R scripts are in the process of being rewritten for packaging with roxygen. For now, they should work but you might need to change some hard-coded function imports and paths to external programs.

The R source code is in R/ and can be built with build_package.r. Pre-compiled packages for Win, Mac, and Unices are also available in compiled/.

Examples and a vignette are forthcoming....

Tested in GNU/Linux. Should also work in OS X and probably in Windows. But note that dependencies are not currently well documented.

PS. Two shell scripts (nex2nwk and rm_node_annotations.py) are also included (in bin/). These can be copied or symlinked into, e.g., $HOME/bin/ for convenient use. You may need to chmod +x them, and the first one probably won't work on Windows as written.