Brownie

Brownie is a program for analyzing rates of continuous character evolution and looking for substantial rate differences in different parts of a tree using likelihood ratio tests and Akaike Information Criterion (AIC) statistics. A manuscript describing the method appears in the May 2006 issue of Evolution. The manual is available here (pdf); see below for info on downloading the program.

There are two versions of the Brownie software. Brownie 1.0 is a set of MATLAB modules. It requires the Stats package for MATLAB and is no longer updated. Brownie 2.0 is a completely rewritten C++ program available as a compiled application for Mac OS X and Windows and also available as source code. Brownie 2.0 can read Nexus tree and data files and can perform analyses across a set of weighted input trees (such as trees weighted by posterior probabilities or bootstrap values) in order to deal with tree uncertainty. While Brownie deals with subtrees (and uses the censored test of O'Meara et al), Sanderson's r8s program can output rate estimates for individual edges or sets of edges and is needed for the non-censored test. Note that Brownie 2.0 uses code (including the useful Nexus Class Library) from Paul Lewis, Rod Page, and the GNU Scientific Library. A version of Brownie now in development will implement some of the branch length adjustments of Blomberg et al (2003) and Pagel's papers and will also implement the non-censored test, plus some other features. Email me if you have any requests, suggestions, or questions.

I ask that you join the Brownie users mailing list when downloading the program so you can be notified about bugs and updates (probably no more than a few times per year). There's also a Brownie support mailing list for active discussions regarding the program. You should also see the Brownie support and suggestions site. Your email address will not be distributed further. You can also anonymously go to the downloads page.

Manuscript describing method:

O'Meara, B.C., C. Ané, M.J. Sanderson, and P.C. Wainwright. Testing for different rates of continuous trait evolution using likelihood. Evolution 60(5): 922-933. PDF.

Papers using Brownie:

Collar, D.C., T.J. Near and P.C. Wainwright. 2005. Comparative analysis of morphological diversity: trophic evolution in centrarchid fishes. Evolution 59(8) 1783-1794. PDF available.
Davis, C.C., M. Latvis, D.L. Nickrent, K.J. Wurdack, and D.A. Baum. 2007. Floral Gigantism in Rafflesiaceae Science DOI: 10.1126/science.1135260