nni: Tree rearrangements.

In phangorn: Phylogenetic Reconstruction and Analysis

Tree rearrangements.

Description

nni returns a list of all trees which are one nearest neighbor interchange away. rNNI and rSPR are two methods which simulate random trees which are a specified number of rearrangement apart from the input tree. Both methods assume that the input tree is bifurcating. These methods may be useful in simulation studies.

Usage

nni(tree)

rNNI(tree, moves = 1, n = length(moves))

rSPR(tree, moves = 1, n = length(moves), k = NULL)

Arguments

tree	A phylogenetic tree, object of class phylo.
moves	Number of tree rearrangements to be transformed on a tree. Can be a vector
n	Number of trees to be simulated.
k	If defined just SPR of distance k are performed.

Value

an object of class multiPhylo.

Author(s)

Klaus Schliep [e-mail]

See Also

allTrees, SPR.dist

Examples

tree <- rtree(20, rooted = FALSE)
trees1 <- nni(tree)
trees2 <- rSPR(tree, 2, 10)

phangorn documentation built on Sept. 17, 2024, 5:08 p.m.