addData                 Adding data to a phylo4 or a phylo4d object
as                      Converting between phylo4/phylo4d and other
                        phylogenetic tree formats
checkPhylo4             Validity checking for phylo4 objects
children                tree traversal and utility functions
extractTree             Get tree from tree+data object
formatData              Format data for use in phylo4d objects
geospiza                Data from Darwin's finches
getNode                 node and edge look-up functions
hasNodeData             Tests for presence of data associated with
                        trees stored as phylo4d objects
hasSingle               Test trees for polytomies, inline nodes, or
                        reticulation
labels<-                Labels for phylo4/phylo4d objects
multiPhylo-class        multiPhylo4 and extended classes
nData                   Retrieves the number of datasets in phylo4d
                        objects
nNodes                  Methods for S4 phylogeny classes
owls4                   'Owls' data from ape
pdata                   Constructor for pdata (phylogenetic data) class
pdata-class             Class "pdata"
phylo4-class            The phylo4 class
phylo4-methods          Create a phylogenetic tree
phylo4d                 Combine a phylogenetic tree with data
phylo4d-class           phylo4d class
phylo4vcov-class        matrix classes for phylobase
phyloXXYY               Calculate node x and y coordinates
phylobase-package       Utilities and Tools for Phylogenetics
phylobase.options       Set or return options of phylobase
phylobubbles            Bubble plots for phylo4d objects
phylog-class            Class "phylog"
plotOneTree             Plot a phylo4 object
print,phylo4-method     Displaying phylo4 object
printphylo4             print a phylogeny
readNexus               Create a phylo4, phylo4d or data.frame object
                        from a Nexus or a Newick file
reorder-methods         reordering trees within phylobase objects
show,phylo4d-method     Display methods for phylo4d objects
subset-methods          Methods for creating subsets of phylogenies
tdata                   Retrieving or updating tip and node data in
                        phylo4d objects
tip.data.plot           Plotting trees and associated data
treePlot                Phylogeny plotting
