ape (version 1.2-7)

root: Roots Phylogenetic Trees

Description

This function reroots a phylogenetic tree with respect to the specified outgroup.

Usage

root(phy, outgroup)

Arguments

phy

an object of class "phylo".

outgroup

a vector of mode numeric or character specifying the tips to delete.

Value

• an object of class "phylo".

Details

The argument outgroup can be either character or numeric. In the first case, it gives the labels of the tips to be deleted; in the second case the numbers of these labels in the vector phy$tip.label are given. If outgroup is of length one (i.e. a single value), then the tree is rerooted using the node below this tip as the new root. If outgroup is of length two or more, the most recent common ancestor (MRCA) is used as the new root. Note that the tree is really unrooted before being rerooted, so that if outgroup is already the outgroup, then the returned tree is not the same than the original one (see examples). If outgroup is not monophyletic, the operation fails and an error message is issued.

See Also

bind.tree, drop.tip

Examples

data(bird.orders)
plot(root(bird.orders, 1))
plot(root(bird.orders, 1:5))

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