Species Tree

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.

Value

The function returns an object of class phylo.

Details

coalSpeciesTree estimates a single linkage tree as suggested by Liu, Yu, and Pearl (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.

References

Liu L, Yu L, Pearl DK (2010). “Maximum tree: A consistent estimator of the species tree.” Journal of Mathematical Biology, 60(1), 95–106. ISSN 0303-6812. doi:10.1007/s00285-009-0260-0 .

See also

speciesTree

Author

Klaus Schliep klaus.schliep@gmail.com Emmanuel Paradies

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)