TreeTools (version 1.6.0)

NJTree: Generate a neighbour joining tree

Description

NJTree() generates a rooted neighbour joining tree from a phylogenetic dataset.

Usage

NJTree(dataset, edgeLengths = FALSE, ratio = TRUE, ambig = "mean")

Arguments

dataset

A phylogenetic data matrix of class phyDat, whose names correspond to the labels of any accompanying tree.

edgeLengths

Logical specifying whether to include edge lengths.

ambig, ratio

Settings of ambig and ratio to be used when computing Hamming() distances between sequences.

Value

NJTree returns an object of class phylo.

See Also

Other tree generation functions: ConstrainedNJ(), GenerateTree, SingleTaxonTree(), TreeNumber

Examples

# NOT RUN {
data('Lobo')
NJTree(Lobo.phy)

# }