Monday, March 7, 2011
Sam Price has created a wiki tutorial for my brownie.lite() function that conducts the rate variation analysis described in O'Meara et al. (2006) and implemented in Brian's C++ program Brownie; and for my function to read stochastic character map formatted trees, read.simmap(). The tutorial is far more detailed than anything that I could have prepared and comes with an empirical example to test. The link to the tutorial is here. The R functions brownie.lite() and read.simmap() are available from my R phylogenetics page (direct links to code are here and here, respectively).