dist.phylo

This function computes the pairwise distances between the pairs of
  tips from a phylogenetic tree using the branch lengths of the latter.

manip

Ape provides functions for reading, and plotting phylogenetic
  trees in parenthetic format (standard Newick format), analyses of
  comparative data in a phylogenetic framework, analyses of diversification
  and macroevolution, computing distances from allelic and nucleotide data,
  reading nucleotide sequences from GenBank via internet, and several tools
  such  as Mantel's test, computation of minimum spanning tree, or the
  population parameter theta based on various approaches.

dist.phylo: Pairwise Distances from a Phylogenetic Tree

Description

Usage

Arguments

Value

See Also