Import Nexus and Newick files
                        Create a 'phylo4', 'phylo4d' or 'data.frame'
                        object from a NEXUS or a Newick file
MRCA                    MRCA
addData                 Adding data to a phylo4 or a phylo4d object
ancestor                Tree traversal and utility functions
checkPhylo4             Validity checking for phylo4 objects
edges                   Edges accessors
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
hasEdgeLength           edgeLength methods
hasSingle               Test trees for polytomies, inline nodes
                        (singletons), or reticulation
hasTipData              Tests for presence of data associated with
                        trees stored as phylo4d objects
isRooted                Methods to test, access (and modify) the root
                        of a phylo4 object.
multiPhylo-class        multiPhylo4 and extended classes
nTips                   nTips, nNodes, nEdges
nodeId                  nodeId methods
owls4                   'Owls' data from ape
pdata                   Constructor for pdata (phylogenetic data) class
pdata-class             Class "pdata"
phylo4-class            The phylo4 class
phylo4-labels           Labels for phylo4/phylo4d objects
phylo4-methods          Create a phylogenetic tree
phylo4d-class           phylo4d class
phylo4d-methods         Combine a phylogenetic tree with data
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
phylomat-class          matrix classes for phylobase
plotOneTree             Plot a phylo4 object
print                   print a phylogeny
reorder-methods         reordering trees within phylobase objects
setAs                   Converting between phylo4/phylo4d and other
                        phylogenetic tree formats
shortestPath            shortestPath-methods
subset-methods          Methods for creating subsets of phylogenies
summary-methods         Summary for phylo4/phylo4d objects
tdata                   Retrieving or updating tip and node data in
                        phylo4d objects
tip.data.plot           Plotting trees and associated data
treePlot-methods        Phylogeny plotting
