tree <- TreeTools::BalancedTree(8)
# A random rearrangement
NNI(tree)
cNNI(tree)
# All trees one NNI rearrangement away
NNI(tree, edgeToBreak = -1)
# Manual random sampling
cNNI(tree, sample.int(14 - 8 - 1, 1), sample.int(2, 1))
# A specified rearrangement
cNNI(tree, 0, 0)
# If a tree may not be binary, collapse nodes with
tree <- TreeTools::MakeTreeBinary(tree)
# If a tree may be improperly rooted, use
tree <- TreeTools::RootTree(tree, 1)
# If a tree may exhibit unusual node ordering, this can be addressed with
tree <- TreeTools::Preorder(tree)
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