<code>cophenetic.phylo</code> computes the pairwise distances between the
  pairs of tips from a phylogenetic tree using its branch lengths.<p></p><p>  <code>dist.nodes</code> does the same but between all nodes, internal and
  terminal, of the tree.</p>

manip

cophenetic.phylo

ape provides functions for reading, writing, plotting, and
        manipulating phylogenetic trees, analyses of comparative data
        in a phylogenetic framework, analyses of diversification and
        macroevolution, computing distances from allelic and nucleotide
        data, reading nucleotide sequences, and several tools such as
        Mantel's test, computation of minimum spanning tree,
        generalized skyline plots, estimation of absolute evolutionary
        rates and clock-like trees using mean path lengths,
        non-parametric rate smoothing and penalized likelihood.
        Phylogeny estimation can be done with the NJ, BIONJ, and ME
        methods.

cophenetic.phylo: Pairwise Distances from a Phylogenetic Tree

Description

Usage

Arguments

Value

See Also