I am trying to estimate speciation and extinction rates for a phylogeny which is near-complete in the backbone (90% of all genera sampled) but very incomplete at the tips (5% of all species sampled). I have used BAMM for this but want to compare the results with those of another method. However, I can't seem to find another method that would do exactly that (plot rates against time estimated from incomplete phylogenies by setting the sampling proportion for each tip). What other method would be recommended if any?
Thanks Florian! I had looked at MEDUSA before BAMM but it seems it cannot test for mass extinction events since the rates over time are held constant. In my case it would actually work since I found a constant extinction rate with BAMM, but I could not have known this a priori.
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