Re: [R-sig-phylo] when not to use an ultrametric tree?

Thanks Brian! Yeah, in correspondence with Trevor Bedford and Simon Blomberg I explored doing a more complex analysis, but in the end because of publication time constraints and current software limitations I settled for 1- and 2-rate BM models fit on a single gene basis. I was really excited ab

Re: [R-sig-phylo] when not to use an ultrametric tree?

If your question were about rates in terms of changes per unit time, then a tree with branches proportional to time (which would be ultrametric for coeval species) would be fairly important. But if your question were about changes per unit of genetic change (or something else, like per generation,

[R-sig-phylo] when not to use an ultrametric tree?

Hi All, I have what I hope is not too basic a question. Under what circumstances is it OK to not use an ultrametric tree for comparative analyses? I'm going to compare the fit of 1- and 2-rate brownian motion models to gene expression data on 4 species for which I have a good but not ultrametri