A model for delimiting species on a rooted phylogenetic tree. PTP model speciations or branching events in terms of number of substitutions. So it only requires a phylogenetic input tree, for example the output of RAxML. It can easily be integrated with the EPA (evolutionary placement algorithm) to calculate the number of species in a set of query sequences that have been placed into a specific branch of the reference phylogeny. We implemented an open reference species delimitation pipeline by integrating PTP with the EPA to identify known and new species.