phangorn (version 0.0-5)

allTrees: Compute all trees topologies and nearest neighbor interchange.

Description

allTrees computes all tree topologies for rooted or unrooted trees with up to 10 tips. nni returns a list of all trees which are one nearest neighbor interchange away. Both methods assume bifurcating trees.

Usage

allTrees(n, rooted = FALSE, tip.label = NULL)
nni(tree,  edge.length = FALSE)

Arguments

n

Number of tips (

rooted

Rooted or unrooted trees (default: rooted).

tip.label

Tip labels.

tree

A phylogenetic tree, object of class phylo.

edge.length

Keep edge lengths?

Value

• an object of class phylo.

See Also

fastme, distanceHadamard

Examples

trees <- allTrees(5)
par(mfrow = c(3,5))
for(i in 1:15)plot(trees[[i]])

neighborhood <- nni(trees[[1]])