R: Species Tree

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 `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 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

`speciesTree`

[Package phangorn version 2.3.1 Index]