R: Tree rearrangements.

nni {phangorn} | R Documentation

## 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 klaus.schliep@gmail.com

### See Also

`allTrees`, `SPR.dist`

### Examples

    tree <- unroot(rtree(20))
    trees1 <- nni(tree)
    trees2 <- rSPR(tree, 2, 10)

[Package phangorn version 2.3.1 Index]