cophenetic.phylo

dist.phylo

a logical indicating whether to return the distances among
    all tips and nodes (if <code>TRUE</code>); the default is to return only
    the distances among tips.

full

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

manip

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, the population
  parameter theta based on various approaches, nucleotide diversity,
  generalized skyline plots, estimation of absolute evolutionary rates
  and clock-like trees using non-parametric rate smoothing, conversion
  of APE trees to and from hclust objects and for classifying genes in
  trees using the Klastorin-Misawa-Tajima approach. Phylogeny estimation
  can be done with the NJ and ML methods.

cophenetic.phylo: Pairwise Distances from a Phylogenetic Tree

Description

Usage

Arguments

Value

See Also