R: Pairwise Distances from a Phylogenetic Tree

cophenetic.phylo {ape} | R Documentation

## Pairwise Distances from a Phylogenetic Tree

### Description

`cophenetic.phylo` computes the pairwise distances between the pairs of tips from a phylogenetic tree using its branch lengths.

`dist.nodes` does the same but between all nodes, internal and terminal, of the tree.

### Usage

    ## S3 method for class 'phylo'
    cophenetic(x)
    dist.nodes(x)

### Arguments

`x` | an object of class `"phylo"`.

### Value

a numeric matrix with colnames and rownames set to the names of the tips (as given by the element `tip.label` of the argument `phy`), or, in the case of `dist.nodes`, the numbers of the tips and the nodes (as given by the element `edge`).

### Author(s)

Emmanuel Paradis

### See Also

`read.tree` to read tree files in Newick format, `cophenetic` for the generic function

[Package ape version 5.0 Index]