coalSpeciesTree: Species Tree

In KlausVigo/phangorn: Phylogenetic Reconstruction and Analysis

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 multiPhylo
X	A phyDat object to define which individual belongs to which species.
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 [e-mail] 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

speciesTree

Examples

## example in Liu et al. (2010)
tr1 <- read.tree(text = "(((B:0.05,C:0.05):0.01,D:0.06):0.04,A:0.1);")
tr2 <- read.tree(text = "(((A:0.07,C:0.07):0.02,D:0.09):0.03,B:0.12);")
TR <- c(tr1, tr2)
sp_tree <- coalSpeciesTree(TR)

KlausVigo/phangorn documentation built on Nov. 5, 2024, 11 a.m.