Rotates a node or set of nodes in a phylogenetic tree
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).
rotateNodes(tree, nodes, polytom=c(1,2), ...) rotate.multi(tree, node) allRotations(tree)
tree |
object of class |
nodes |
either a single node number to rotate, a vector of node numbers, or the string |
polytom |
a vector of mode numeric and length two specifying the two clades that should be exchanged in a polytomy (see |
node |
a single node to rotate (in the case of |
... |
optional arguments. |
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.
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.
Liam Revell liam.revell@umb.edu
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.
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