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"
ExpectedLength          Expected length
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.
MostContradictedFreq    Frequency of most common contradictory split
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
PresCont                Group present or contradicted score
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
