Exercises for PAUP*, with emphasis on model selection
The data set we will use for this exercise is called simulated-dna-data.nex and can be downloaded from the workshop web site here. It is a simulated data set consisting of DNA sequences for 9 organisms and 2500 sites (taxon 9 is the outgroup). I won’t give much more than that about the simulation conditions, but you can assume that the simulation was a homogenous Markov process (i.e., all sites evolving according to the same model, and the model does not change over the tree).
In this key, (terse) answers to the questions are shown in boldface. Lines beginning with “paup> “ are PAUP* input command lines.