The whole-tree tests of diversification rate variation described in Chan and Moore (2003, "Whole tree methods for detecting differential diversification rates", see PAPERS)--Mr, Mp, and Ms, along with Colless' Ic and Shao and Sokal's B1--have been implemented in SymmeTREE, a command line controlled program written in ANSI C++. A recent version of the program also implements shift statistics for identifying potential shifts in diversification rates, as explained in Moore et al. (2004, "Detecting diversification rate variation in supertrees", see PAPERS). Executables have been compiled for Windows, Linux, and Macintosh operating systems, which are freely available via the WWW at http://www.phylodiversity.net/bmoore/software.html. A detailed manual is now also available. (Please notify me at kaichan@stanford.edu if you will be using SymmeTREE, and which version you will be using, so that I can notify you of the appropriate updates and new developments.) SymmeTREE accepts input Nexus files, or simple text files with trees in standard parenthetical notation, such as that used by Newick and Nexus formats. Results of analyses are output as tab-delimited text files, which are easily exported to spreadsheet programs.

A major impetus in developing the whole-tree methods is to capitalize on recent and anticipated advances in supertree estimation, which promise to provide exceptionally large and complete phylogenies for the study of differential diversification rates. Despite their obvious advantages, supertrees often contain a considerable proportion of unresolved nodes (although perhaps no more so than trees estimated by primary analysis: Bininda-Emonds and Sanderson, 2001). Because methods for detecting diversification rate variation typically require strictly dichotomous trees, the empirical reality of polytomies has proven to be a serious impediment to their analysis. Accordingly, SymmeTREE has a number of facilities for analyzing trees that are incompletely resolved. For example, a suite of algorithms allow polytomies to be randomly (and repeatedly) resolved under conditions conforming to an ERM model, providing an estimate of the confidence intervals on the whole-tree probabilities obtained under the various statistics.

Alternatively, when polytomies are a result of conflicting data, rather than a lack of it, the polytomies are points of "consensus". Where the random resolution method above assumes that each resolution is equally well supported, often several resolutions of the consensus polytomy are equally well supported, while others are less well supported. The random resolution of consensus trees would therefore represent a significant loss of information. Accordingly, SymmeTREE does not require single consensus trees: it can process sets of equally optimal trees as a batch, recording and outputting frequentiles/confidence intervals for the various symmetry statistics. A formal account of the algorithms involved in treating polytomies may be found in Chan and Moore (in prep., SymmeTREE: An application for performing whole tree tests of diversification rate variation, see PAPERS).