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