ape (version 1.8-1)

root: Roots Phylogenetic Trees

Description

root reroots a phylogenetic tree with respect to the specified outgroup.

unroot unroots a phylogenetic tree, or returns it unchanged if it is already unrooted.

is.rooted tests whether a tree is rooted.

Usage

root(phy, outgroup)
unroot(phy)
is.rooted(phy)

Arguments

phy

an object of class "phylo".

outgroup

a vector of mode numeric or character specifying the new outgroup.

Value

• an object of class "phylo" for root and unroot; a logical for is.rooted.

Details

The argument outgroup can be either character or numeric. In the first case, it gives the labels of the tips of the new outgroup; 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.

A tree is considered rooted if either only two branches connect to the root, or if there is a root.edge element. In all other cases, is.rooted returns FALSE.

See Also

bind.tree, drop.tip, rotate

Examples

data(bird.orders)

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

is.rooted(bird.orders) # yes!
is.rooted(root(bird.orders, 1)) # no!
### This is because the tree has been unrooted first before re-rooting.
### You can delete the outgroup...
is.rooted(drop.tip(root(bird.orders, 1), "Struthioniformes"))
### ... or resolve the basal trichotomy:
is.rooted(multi2di(root(bird.orders, 1)))
### To keep the basal trichotomy but forcing the tree as rooted:
tr <- root(bird.orders, 1)
tr$root.edge <- 0
is.rooted(tr)