TreeSearch1.5.1 package

Find most parsimonious trees

Parsimony Ratchet

Addition tree

All SPR trees

Number of trees with m steps

Character length

Cluster similar strings

Evaluate the concordance of information between a tree and a dataset

Consistency / retention "indices"

cSPR() expects a tree rooted on a single tip.

Combine two edge matrices

Translate a gap treatment into a string in the format expected by Morp...

Non-duplicate root

Unique trees (ignoring "hits" attribute)

Double NNI

TBR Warning Print a warning and return given tree

Read how a Morphy Object handles the inapplicable token

Is an object a valid Morphy object?

Jackknife resampling

Label nodes with jackknife support values

Contribution of character to leaf instability

Calculate the parsimony score of a tree given a dataset

Minimum and Maximum lengths possible for a character

Check for error whilst modifying Morphy object

Calculate parsimony score from Morphy object

Set and get the character weightings associated with a Morphy object.

Commits parameters prior to nodal set calculations.

Search for most parsimonious trees

Attach raw character state data (i.e. tip data).

Attach a caller-specified list of symbols.

Destroys an instance of a Morphy object.

Deletes the caller-input data.

Reconstructs the first (downpass) nodal reconstructions

Reconstructs the second (uppass) nodal reconstructions.

Retrieve the weight of a character in the dataset

Get / set gap handler from a Morphy object.

Retrieve the number of character (columns) in the dataset.

Gets the number of internal nodal reconstruction sets being used by Mo...

Retrieve the number of taxa (rows) in the dataset.

Retrieves the current list of symbols.

Sets up the dimensions of the dataset.

Creates a new instance of a Morphy object

Performs the second nodal reconstructions for characters with inapplic...

Finalises the ancestral state reconstructions for characters with inap...

Set the weight of a character in the dataset

Sets the number of internal nodes in the dataset

Sets a character's parsimony function type

Converts a numeric error code to human-readable format

Updates the nodal sets for a lower ("dummy") root node

Initial update of tip values following uppass reconstruction.

Nearest neighbour interchange (NNI)

Initialize a Morphy object from a phyDat object

Plot the distribution of a character on a tree

Prepare data for Profile Parsimony

Relationship between four taxa

Random postorder tree

Parsimony score of random postorder tree

Rearrange edges of a phylogenetic tree

Morphy object from single character

Calculate site concordance factor

Subtree pruning and rearrangement (SPR)

Information content of a character known to contain e steps

Check that all nodes in a tree are bifurcating.

Tree suboptimality

Tree search using successive approximations

Details the attributes of a morphy object

Rank taxa by their influence on phylogenetic results

Tree bisection and reconnection (TBR)

Destroy a Morphy object

When was a tree topology first hit?

Number of trees with one extra step