TBR performs a single random TBR iteration.

TBR(tree, edgeToBreak = NULL, mergeEdges = NULL)

TBRMoves(tree, edgeToBreak = integer(0))

# S3 method for phylo
TBRMoves(tree, edgeToBreak = integer(0))

# S3 method for matrix
TBRMoves(tree, edgeToBreak = integer(0))

TBRSwap(
parent,
child,
nEdge = length(parent),
edgeToBreak = NULL,
mergeEdges = NULL
)

RootedTBR(tree, edgeToBreak = NULL, mergeEdges = NULL)

RootedTBRSwap(
parent,
child,
nEdge = length(parent),
edgeToBreak = NULL,
mergeEdges = NULL
)

## Arguments

tree

A bifurcating tree of class phylo, with all nodes resolved;

edgeToBreak

(optional) integer specifying the index of an edge to bisect/prune, generated randomly if not specified. Alternatively, set to -1 to return a complete list of all trees one step from the input tree.

mergeEdges

(optional) vector of length 1 or 2, listing edge(s) to be joined: In SPR, this is where the pruned subtree will be reconnected. In TBR, these edges will be reconnected (so must be on opposite sides of edgeToBreak); if only a single edge is specified, the second will be chosen at random

parent

Integer vector corresponding to the first column of the edge matrix of a tree of class phylo, i.e. tree$edge[, 1]. child Integer vector corresponding to the second column of the edge matrix of a tree of class phylo, i.e. tree$edge[, 2].

nEdge

(optional) Number of edges.

## Value

This function returns a tree in phyDat format that has undergone one TBR iteration.

TBRMoves() returns a multiPhylo object listing all trees one TBR move away from tree, with edges and nodes in preorder, rooted on the first-labelled tip.

a list containing two elements, corresponding in turn to the rearranged parent and child parameters

## Details

Branch lengths are not (yet) supported.

All nodes in a tree must be bifurcating; ape::collapse.singles and ape::multi2di may help.

## Functions

• TBRSwap: faster version that takes and returns parent and child parameters

• RootedTBR: Perform TBR rearrangement, retaining position of root

• RootedTBRSwap: faster version that takes and returns parent and child parameters

## References

The TBR algorithm is summarized in Felsenstein J (2004). Inferring phylogenies. Sinauer Associates, Sunderland, Massachusetts.

RootedTBR(): useful when the position of the root node should be retained.

Other tree rearrangement functions: NNI(), SPR()

Martin R. Smith

## Examples

{
library('ape')
tree <- rtree(20, br=NULL)
TBR(tree)
}
#>
#> Phylogenetic tree with 20 tips and 19 internal nodes.
#>
#> Tip labels:
#>   t12, t4, t10, t13, t15, t9, ...
#>
#> Rooted; no branch lengths.