PRANC

PRANC computes probabilities of ranked and unranked gene tree topologies and estimates maximum-likelihood species trees under the multispecies coalescent model.

Key Features:

• Probability computation: Calculates probabilities of ranked or unranked gene tree topologies given a species tree under the multispecies coalescent.
• Support for ranked gene trees: Handles ranked gene trees that encode the temporal sequence of coalescent events in addition to topology.
• Maximum likelihood species-tree estimation: Estimates ML species trees from samples of ranked or unranked gene tree topologies and reports branch lengths in coalescent units.
• Starting tree options: Accepts starting trees such as greedy consensus trees or trees selected by minimization of ancient coalescence (MAC).
• Democratic vote topologies: Outputs the most frequent (democratic vote) ranked or unranked tree topologies observed in a dataset.

Scientific Applications:

• Species tree inference: Estimating species trees from collections of gene tree topologies under the multispecies coalescent.
• Divergence time inference: Recovering relative divergence information via branch lengths expressed in coalescent units.
• Temporal resolution of coalescence: Using ranked gene trees to capture the ordering of coalescent events for finer evolutionary inference.
• Genealogical summary: Summarizing gene tree distributions using democratic vote topologies to identify prevalent genealogical patterns.

Methodology:

Computes probabilities of ranked and unranked gene tree topologies given a species tree under the multispecies coalescent; performs maximum-likelihood estimation of species trees from samples of ranked or unranked gene tree topologies with branch lengths in coalescent units; supports starting trees such as greedy consensus or minimization of ancient coalescence (MAC); and outputs democratic vote topologies.