Root or unroot a phylogenetic tree

RootTree() roots a tree on the smallest clade containing the specified tips; RootOnNode() roots a tree on a specified internal node; UnrootTree() collapses a root node, without the undefined behaviour encountered when using ape::unroot() on trees in preorder.

Usage

RootTree(tree, outgroupTips, fallback = NULL)

RootOnNode(tree, node, resolveRoot = FALSE)

UnrootTree(tree)

Arguments

tree

A tree of class phylo, or a list of trees of class list or multiPhylo.

outgroupTips

Vector of type character, integer or logical, specifying the names or indices of the tips to include in the outgroup. If outgroupTips is a of type character, and a tree contains multiple tips with a matching label, the first will be used.

fallback

Vector corresponding to outgroupTips determining behaviour when outgroupTips do not root a tree.

Where the smallest clade that contains outgroupTips includes all taxa, RootTree() will not change the topology of a tree. If fallback = NULL, RootTree() will return tree. Otherwise, taxa will be excluded from outgroupTips in the sequence specified (fallback[1] first) by until the clade containing all outgroup tips is smaller than tree.

node

Integer specifying node (internal or tip) to set as the root.

resolveRoot

Logical specifying whether to resolve the root node.

Value

RootTree() returns a tree of class phylo, rooted on the smallest clade that contains the specified tips, with edges and nodes numbered in preorder. Node labels are not retained.

RootOnNode() returns a tree of class phylo, rooted on the requested node and ordered in Preorder.

UnrootTree() returns tree, in preorder, having collapsed the first child of the root node in each tree.

See also

• ape::root()

Other tree manipulation: AddTip(), CollapseNode(), ConsensusWithout(), DropTip(), ImposeConstraint(), KeptPaths(), KeptVerts(), LeafLabelInterchange(), MakeTreeBinary(), Renumber(), RenumberTips(), RenumberTree(), SortTree(), Subtree(), TipTimedTree(), TrivialTree

Author

Martin R. Smith (martin.smith@durham.ac.uk)

Examples

tree <- PectinateTree(8)
plot(tree)
ape::nodelabels()


plot(RootTree(tree, c("t6", "t7")))


plot(RootOnNode(tree, 12))

plot(RootOnNode(tree, 2))