phangorn: nni – R documentation

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nni

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

Examples

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

phangorn

Phylogenetic Reconstruction and Analysis

v2.7.0

GPL (>= 2)

Authors

Klaus Schliep [aut, cre] (<https://orcid.org/0000-0003-2941-0161>), Emmanuel Paradis [aut] (<https://orcid.org/0000-0003-3092-2199>), Leonardo de Oliveira Martins [aut] (<https://orcid.org/0000-0001-5247-1320>), Alastair Potts [aut], Tim W. White [aut], Cyrill Stachniss [ctb], Michelle Kendall [ctb], Keren Halabi [ctb], Richel Bilderbeek [ctb], Kristin Winchell [ctb], Liam Revell [ctb], Mike Gilchrist [ctb], Jeremy Beaulieu [ctb], Brian O'Meara [ctb], Long Qu [ctb]

Initial release

nni