A program to compute probabilities of ranked gene tree topologies in species trees

by Islam Ismailov for National Evolutionary Synthesis Center

A polynomial-time algorithm has been described for computing probabilities of ranked gene tree topologies given species trees. Once, implemented, ranked gene tree probabilities could be used to infer species trees, although inferring species trees is beyond the scope of the project. The idea is to consider ranked gene tree topologies, where we distinguish the relative order of times of nodes on gene trees, but not the real-valued branch lengths.