coalSpeciesTree {phangorn} | R Documentation |
Species Tree
Description
coalSpeciesTree
estimates species trees and can handle multiple
individuals per species.
Usage
coalSpeciesTree(tree, X = NULL, sTree = NULL)
Arguments
tree |
an object of class |
X |
A |
sTree |
A species tree which fixes the topology. |
Details
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.
Value
The function returns an object of class phylo
.
Author(s)
Klaus Schliep klaus.schliep@gmail.com Emmanuel Paradies
References
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.
See Also
[Package phangorn version 2.11.1 Index]