TreeTools

Add a tip to a phylogenetic tree

Ancestral edge

Read modification time from 'ape' Nexus file

Artificial Extinction

Character information content

Clade sizes

Cladistic information content of a tree

Collapse nodes on a phylogenetic tree

Which splits are compatible?

Consensus without taxa

Identify descendant edges

Double factorial

Drop tips from tree

Ancestors of an edge

Distance between edges

Generate a tree with a specific outgroup

Extract taxa from a matrix block

Generate pectinate, balanced or random trees

Label splits

Leaf label interchange

List ancestors

Data from Zhang et al. 2016

Most recent common ancestor

Minimum spanning tree

Generate binary tree by collapsing polytomies

Convert between matrices and phyDat objects

Number of trees one SPR step away

Count descendants for each node in a tree

Generate a neighbour joining tree

Distributions of tips consistent with a partition pair

Number of trees

Number of distinct splits

Number of leaves in a phylogenetic tree

Write Newick Tree

Reorder edges of a phylogenetic tree

Distance of each node from tree exterior

Order of each node in a tree

Non-duplicate root

Distances between each pair of trees

Convert between strings and phyDat objects

Read phylogenetic characters from file

Parse TNT Tree

Renumber a tree's nodes and tips

Renumber a tree's tips

Reorder trees

Rightmost character of string

Which node is a tree's root?

Root or unroot a phylogenetic tree

Quickly sample

Generate a single taxon tree

Sort tree

Frequency of splits

Phylogenetic information content of splitting leaves into two partitions

Probability of matching this well

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

Tips contained within splits

Total Cophenetic Index

Is tree rooted?

Unique integer indices for bifurcating tree topologies

Integer representing shape of a tree

TreeTools

Number of trees matching a bipartition split

Number of trees containing a tree

Identify and remove trivial splits

Number of trees consistent with split

Add tree to start of list

Write morphological character matrix to TNT file

Write a phylogenetic tree in Newick format

Convert object to Splits

Convert object to multiPhylo class

Brewer palettes

Random parent vector

Double factorials

Natural logarithms of double factorials

Split matching

Number of rooted / unrooted tree shapes

Print TreeNumber object

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