rotateNodes: Rotates a node or set of nodes in a phylogenetic tree

In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

Rotates a node or set of nodes in a phylogenetic tree

Description

The function rotateNodes is a simple wrapper for rotate which rotates a set of nodes or all nodes.

The function rotate.multi finds all possible rotations around a multifurcating node, given by node. This will be an object of class "multiPhylo", assuming that the node specified is indeed a multifurcation.

The function allRotations computes all possible rotated trees for a given input phylogeny. For a binary tree, this is generally two raised to the power of the number of internal nodes (so a very large number, if N is even modest in size).

Usage

rotateNodes(tree, nodes, polytom=c(1,2), ...)
rotate.multi(tree, node)
allRotations(tree)

Arguments

tree	object of class "phylo".
nodes	either a single node number to rotate, a vector of node numbers, or the string "all".
polytom	a vector of mode numeric and length two specifying the two clades that should be exchanged in a polytomy (see rotate).
node	a single node to rotate (in the case of rotate.multi).
...	optional arguments.

Details

All three functions also address the problem that the product of multiple rotations from rotate can be non-compliant with the implicit "phylo" standard because the tip numbers in tree$edge are not in numerical order 1:n for n tips.

Value

An object of class "phylo" (i.e., a phylogenetic tree), in the case of rotateNodes, or an object of class "multiPhylo" for rotate.multi or allRotations.

Author(s)

Liam Revell [e-mail]

References

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

phytools documentation built on June 22, 2024, 10:39 a.m.