PRANC: ML species tree estimation from the ranked gene trees under coalescence.

Abstract

PRANC computes the Probabilities of RANked gene tree topologies under the multispecies coalescent. A ranked gene tree is a gene tree accounting for the temporal ordering of internal nodes. PRANC can also estimate the maximum likelihood (ML) species tree from a sample of ranked or unranked gene tree topologies. It estimates the ML tree with estimated branch lengths in coalescent units. PRANC is written in C++ and freely available at github.com/anastasiiakim/PRANC. Supplementary data are available at Bioinformatics online.