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