How do I tell paup to use site-specific rates that I have already estimated?
How do I tell paup to use site-specific rates that I have already estimated? You can do this a couple of different ways. The first way is to estimate the rates on a given tree and then apply the estimated rates by using the previous option. In the following example, a character partition defines three genes and the site specific rates for each gene are estimated on a neighbor joining tree. Finally, a heuristic search is executed using the site-specific rates estimated on the neighbor joining tree.
