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Tree bisection and reconnection (TBR)

Source: R/TBR.R
TBR.Rd

TBR performs a single random TBR iteration.

Usage

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

TBRMoves(tree, edgeToBreak = integer(0))

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

# S3 method for class '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

TBR() 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.

TBRSwap() returns a list containing two elements corresponding 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.

See also

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

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

Author

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

Examples

library("ape")
tree <- rtree(20, br=NULL)
TBR(tree)
#> 
#> Phylogenetic tree with 20 tips and 19 internal nodes.
#> 
#> Tip labels:
#>   t13, t19, t7, t18, t1, t20, ...
#> 
#> Rooted; no branch length.