Hi Emmanuel.
Right. Also thank you for your informative answer. I am interested in
keeping the "surviving species" from phylogenies. However, I don't want to
simulate trees.
For example, one of my trees is like this:
Hi Elvira,
If you are interested in keeping the "surviving species" from phylogenies, it
may be better to use a birth-death model to simulate the trees. There are 3
functions in ape to do this: they are documented in the same help page than
drop.fossil() and they have options that make them
