AdditionTree            Addition tree
AllSPR                  All SPR trees
Carter1                 Number of trees with _m_ steps
CharacterLength         Character length
ClusterStrings          Cluster similar strings
ConcordantInformation   Evaluate the concordance of information between
                        a tree and a dataset
Consistency             Consistency / retention "indices"
GapHandler              Read how a Morphy Object handles the
                        inapplicable token
IWScore                 Calculate the parsimony score of a tree given a
                        dataset
JackLabels              Label nodes with jackknife support values
Jackknife               Jackknife resampling
LengthAdded             Contribution of character to leaf instability
MaximizeParsimony       Find most parsimonious trees
MinimumLength           Minimum and Maximum lengths possible for a
                        character
MorphyBootstrap         Parsimony Ratchet
MorphyWeights           Set and get the character weightings associated
                        with a Morphy object.
NNI                     Nearest neighbour interchange (NNI)
PhyDat2Morphy           Initialize a Morphy object from a 'phyDat'
                        object
PlotCharacter           Plot the distribution of a character on a tree
PrepareDataProfile      Prepare data for Profile Parsimony
QuartetResolution       Relationship between four taxa
RandomMorphyTree        Random postorder tree
RandomTreeScore         Parsimony score of random postorder tree
RearrangeEdges          Rearrange edges of a phylogenetic tree
SPR                     Subtree pruning and rearrangement (SPR)
SingleCharMorphy        Morphy object from single character
SiteConcordance         Calculate site concordance factor
StepInformation         Information content of a character known to
                        contain _e_ steps
TBR                     Tree bisection and reconnection (TBR)
TaxonInfluence          Rank taxa by their influence on phylogenetic
                        results
UnloadMorphy            Destroy a Morphy object
WhenFirstHit            When was a tree topology first hit?
WithOneExtraStep        Number of trees with one extra step
cSPR                    'cSPR()' expects a tree rooted on a single tip.
congreveLamsdellMatrices
                        100 simulated data matrices
inapplicable.datasets   Thirty datasets with inapplicable data
is.morphyPtr            Is an object a valid Morphy object?
profiles                Empirically counted profiles for small trees
referenceTree           Tree topology for matrix simulation
summary.morphyPtr       Details the attributes of a morphy object
