index.RmdWe did some model exercises with the molecular data in PAUP. Try applying some of these models to the Barden morphological dataset. What nst values can you use?
If you look at the model output, it says the state space is variable. Take a look at the Barden data file. To what does the “variable” state space refer?
Try choosing a different base frequency. What does PAUP tell you? Try doing as it suggests. Can you figure out what ‘genFreq’ is?
What is the score of the best tree you found? No right answers; winner gets nothing.
We talked about heuristics this week and last. Is a heuristic guaranteed find you the best tree? How are you, personally, going to make peace with this in your work?