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. It now also implements many other methods for examining trait evolution and methods for doing species delimitation. 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 It requires the Stats package for MATLAB and is no longer updated.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 also available as source code. Brownie 2.1 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 as well as species delimitation. Note that Brownie 2.1 uses code (including the useful Nexus Class Library) from Paul Lewis, Rod Page, and the GNU Scientific Library.
You can download the relevant files from the Google Code Brownie site.
Sam Price has prepared a great tutorial/intro to Brownie as part of the Bodega Applied Phylogenetics Workshop. Thanks, Sam!
Note that the continuous trait method that is part of Brownie has been coded in the OUwie and phytools packages in R. However, these only implement the noncensored test.
The latest version was released on 18 November 2009, (3 years, 6 months, 5 days ago)
Subscribe to brownie-announce (group for new program releases and bug alerts, extremely low traffic).
Strongly recommended for all downloaders.
Subscribe to brownie-users (group for help discussions with the program author and other users).