View source: R/treeRearrangement.R
nni | R Documentation |
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.
nni(tree)
rNNI(tree, moves = 1, n = length(moves))
rSPR(tree, moves = 1, n = length(moves), k = NULL)
tree |
A phylogenetic |
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. |
an object of class multiPhylo.
Klaus Schliep klaus.schliep@gmail.com
allTrees
, SPR.dist
tree <- rtree(20, rooted = FALSE)
trees1 <- nni(tree)
trees2 <- rSPR(tree, 2, 10)
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