coalSpeciesTree estimates species trees and can handle multiple
individuals per species.
coalSpeciesTree(tree, X = NULL, sTree = NULL)an object of class multiPhylo
A phyDat object to define which individual belongs to which
species.
A species tree which fixes the topology.
The function returns an object of class phylo.
coalSpeciesTree estimates a single linkage tree as suggested by Liu
et al. (2010) from the element wise minima of the cophenetic matrices of the
gene trees. It extends speciesTree in ape as it allows that have
several individuals per gene tree.
Liu, L., Yu, L. and Pearl, D. K. (2010) Maximum tree: a consistent estimator of the species tree. Journal of Mathematical Biology, 60, 95--106.