TreeTools1.12.0 package

Add a tip to a phylogenetic tree

Random parent vector

Ancestral edge

Read modification time from "ape" Nexus file

Artificial Extinction

Convert object to multiPhylo class

Write a phylogenetic tree in Newick format

Character information content

Clade sizes

Cladistic information content of a tree

S3 methods for ClusterTable objects

Convert phylogenetic tree to ClusterTable

Collapse nodes on a phylogenetic tree

Which splits are compatible?

Construct consensus trees

Reduced consensus, omitting specified taxa

Constrained neighbour-joining tree

Identify descendant edges

Double factorial

Double factorials

Drop leaves from tree

Efficiently convert edge matrix to splits

Ancestors of an edge

Distance between edges

Add full stop to end of a sentence

Generate a tree with a specified outgroup

Extract taxa from a matrix block

Generate pectinate, balanced or random trees

Tips contained within splits

Hamming distance between taxa in a phylogenetic dataset

Force a tree to match a constraint

Is an object a TreeNumber object?

Robust universal tree balance index

Paths present in reduced tree

Identify vertices retained when leaves are dropped

Label splits

Leaf label interchange

List ancestors

Data from Zhang et al. 2016

Natural logarithms of double factorials

Generate binary tree by collapsing polytomies

Split matching

Match nodes and edges between trees

Convert between matrices and phyDat objects

Decode MorphoBank text

Most recent common ancestor

Minimum spanning tree

Number of trees one SPR step away

Count descendants for each node in a tree

Write Newick Tree

Reorder edges of a phylogenetic tree

Generate a neighbour joining tree

Distance of each node from tree exterior

Numeric index of each node in a tree NodeNumbers() returns a sequenc...

Number of edges incident to each node in a tree

Distributions of tips consistent with a partition pair

Number of trees

Number of distinct splits

Number of leaves in a phylogenetic tree

Distances between each pair of trees

Calculate length of paths between each pair of vertices within tree

Convert between strings and phyDat objects

Polarize splits on a single taxon

Print TreeNumber object

Read phylogenetic characters from file

Read posterior tree sample produced by MrBayes

Parse TNT Tree

Renumber a tree's nodes and tips

Renumber a tree's tips

Reorder tree edges and nodes

Rightmost character of string

Visualize position of rogue taxa

Wrapper for internal C function root_on_node()

Which node is a tree's root?

Root or unroot a phylogenetic tree

Quickly sample

Apply a function that returns 64-bit integers over a list or vector

Sort a list of phylogenetic trees

Sort tree

Produce a legend for continuous gradient scales

Frequency of splits

Phylogenetic information content of splitting leaves into two partitio...

Probability of matching this well

Convert object to Splits

Maximum splits in an n-leaf tree

"Stemwardness" of a leaf

Subset of a split on fewer leaves

Extract a subtree

Colour for node support value

Extract tip labels

Display time-calibrated tree using tip information only

Remove metadata from trees

Total Cophenetic Index

Is tree rooted?

Unique integer indices for bifurcating tree topologies

Integer representing shape of a tree

Number of trees matching a bipartition split

Number of trees containing a tree

TreeTools

Identify and remove trivial splits

Generate trivial trees

Remove quotation marks from a string

Number of trees consistent with split

Add tree to start of list

Write morphological character matrix to TNT file

Exclusive OR operation