Plot the distribution of a character on a tree
Random postorder tree
Prepare data for Profile Parsimony
Calculate the parsimony score of a tree given a dataset
Calculate site concordance factor
Information content of a character known to contain e steps
When was a tree topology first hit?
Search for most parsimonious trees
Parsimony score of random postorder tree
Rearrange edges of a phylogenetic tree
Contribution of character to leaf instability
Destroy a Morphy object
Parsimony Ratchet
Unique trees (ignoring "hits" attribute)
100 simulated data matrices
Thirty datasets with inapplicable data
Combine two edge matrices
Tree search using successive approximations
TBR Warning
Print a warning and return given tree
Relationship between four taxa
Attach a caller-specified list of symbols.
Attach raw character state data (i.e. tip data).
Retrieve the number of taxa (rows) in the dataset.
Retrieves the current list of symbols.
Rank taxa by their influence on phylogenetic results
Retrieve the number of character (columns) in the dataset.
Set the weight of a character in the dataset
Initial update of tip values following uppass reconstruction.
Sets a character's parsimony function type
Converts a numeric error code to human-readable format
Morphy object from single character
Subtree pruning and rearrangement (SPR)
mpl_get_num_internal_nodes
Gets the number of internal nodal reconstruction sets being used by
MorphyLib.
mpl_set_num_internal_nodes
Sets the number of internal nodes in the dataset
Check that all nodes in a tree are bifurcating.
Tree bisection and reconnection (TBR)
Number of trees with one extra step
cSPR() expects a tree rooted on a single tip.
Updates the nodal sets for a lower ("dummy") root node
Tree suboptimality
Translate a gap treatment into a string in the format expected by Morphy
Non-duplicate root
Reconstructs the second (uppass) nodal reconstructions.
Is an object a valid Morphy object?
Details the attributes of a morphy object
Finalises the ancestral state reconstructions for characters with
inapplicable values.
Reconstructs the first (downpass) nodal reconstructions
Performs the second nodal reconstructions for characters with
inapplicability.
Commits parameters prior to nodal set calculations.
Destroys an instance of a Morphy object.
Sets up the dimensions of the dataset.
Creates a new instance of a Morphy object
Deletes the caller-input data.
Tree topology for matrix simulation
Empirically counted profiles for small trees
Retrieve the weight of a character in the dataset
Get / set gap handler from a Morphy object.
Cluster similar strings
Read how a Morphy Object handles the inapplicable token
Double NNI
Addition tree
All SPR trees
Character length
Label nodes with jackknife support values
Consistency / retention "indices"
Evaluate the concordance of information between a tree and a dataset
Number of trees with m steps
Initialize a Morphy object from a phyDat object
Jackknife resampling
Check for error whilst modifying Morphy object
Find most parsimonious trees
Nearest neighbour interchange (NNI)
Minimum and Maximum lengths possible for a character
Set and get the character weightings associated with a Morphy object.
Calculate parsimony score from Morphy object