rvosa
commented
8 years ago Also, it is not incredibly obvious where to place a stem fossil on a gene family tree. On a species tree you might say that it places a minimum age constraint on the parent node, but if the parent node is a gene duplication then you can't. Keep drilling down until the parent is a speciation node?
We now only place fossils where the internal node label applied by TreeFAM exactly matches one returned by FossilCalibrations. This is very wasteful: many fossils are omitted. Unfortunately, the FC API seems to return all the fossils nested inside a given clade (is this also true when a species pair is provided?). There might be an algorithmic solution to this: in a post-order traversal, only attach those calibration point IDs we haven't seen yet.