phylobase

The phylobase package seeks to provide a set of S4 classes and methods for representing and manipulating phylogenetic trees and data in R.

Package resources

To install the current release version (0.6.1, rev. 804) use CRAN

To install the nightly snapshot (on a good day, when they build properly) go to the phylobase build page.

The latest version of the source code is always available via Subversion:
svn checkout svn://svn.r-forge.r-project.org/svnroot/phylobase

Where can I find help?

phylobase comes with two vignettes that will help you to get started:

phylo4: classes and methods for phylogenetic trees and data [pdf] gives an overview of the tree manipulation and plotting functions available in phylobase. Also here [pdf].
A developers guide for contributing to phylobase [pdf] provides information about the organization of the package and how to use Subversion. Also here [pdf].

You can contact us on our mailing list. Alternatively, you can send an email the special interest group mailing list on phylogenetic and comparative methods and analyses: R-sig-phylo.

Additional information

The project summary page can found here.
Much of the plotting code was written as part of the 2008 Google Summer of Code
project description and progress can be found here.