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Tree rearrangements.

Source: R/treeRearrangement.R
nni.Rd

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.

See also

allTrees, SPR.dist

Author

Klaus Schliep klaus.schliep@gmail.com

Examples


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