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
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
