Description Usage Arguments Details Value Author(s) References Examples

Given a phylogenetic tree, computes the cophenetic balance index of that phylogenetic tree.

1 | ```
cophen.index(tree, norm = FALSE)
``` |

`tree` |
a single phylogenetic tree. It can be entered as a string the Newick format, as a 'phylo' object ( |

`norm` |
a logical variable that indicates whether the index should be normalized or not. |

The cophenetic index is computed as the sum of the depths of the least common ancestor (LCA) of every pair of leaves.

A numeric value.

Lucia Rotger

A. Mir, F. Rossello, L.Rotger, A new balance index for phylogenetic trees. *Mathematical Biosciences* **241** (2013), 125-136.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | ```
# Computation of the cophenetic balance index of trees
# entered in newick format:
cophen.index("(1,2,3,4,5);")
cophen.index("(1,(2,(3,(4,5))));")
# Computation of the cophenetic balance index of trees
# entered as a phylo object:
require(ape)
random.tree = rtree(5,rooted=TRUE)
cophen.index(random.tree)
# Computation of the cophenetic balance index of a tree
# entered as a igraph object. The tree is randomly
# generated from all trees with 5 leaves following
# the alpha-gamma model with alpha=0.5 and gamma=0.3.
a.g.tree = a.g.model(5,0.5,0.3)
cophen.index(a.g.tree)
#All of them can be normalized (values between 0 and 1)
cophen.index("(1,2,3,4,5);",norm=TRUE)
cophen.index("(1,(2,(3,(4,5))));",norm=TRUE)
cophen.index(random.tree,norm=TRUE)
cophen.index(a.g.tree,norm=TRUE)
``` |

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