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.
# S3 method for phylo
cophenetic(x)
dist.nodes(x, fail.if.no.length = FALSE)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).
an object of class "phylo".
a logical values. If the tree has no branch
lengths, these are all fixed to one (with a warning) so the
computation is done. If you prefer to catch the case of no branch
lengths with an error, set this option to TRUE.
Emmanuel Paradis
read.tree to read tree files in Newick format,
cophenetic for the generic function