GenerateTree: Generate pectinate, balanced or random trees

In TreeTools: Create, Modify and Analyse Phylogenetic Trees

Generate pectinate, balanced or random trees

Description

RandomTree(), PectinateTree(), BalancedTree() and StarTree() generate trees with the specified shapes and leaf labels.

Usage

RandomTree(tips, root = FALSE, nodes, lengths = NULL)

YuleTree(tips, addInTurn = FALSE, root = TRUE, lengths = NULL)

PectinateTree(tips, lengths = NULL)

BalancedTree(tips, lengths = NULL)

StarTree(tips, lengths = NULL)

Arguments

tips	An integer specifying the number of tips, or a character vector naming the tips, or any other object from which TipLabels() can extract leaf labels.
root	Character or integer specifying tip to use as root; or TRUE to root the tree on a random edge; or FALSE to return an unrooted tree.
nodes	Number of nodes to generate. The default and maximum, tips - 1, generates a binary tree; setting a lower value will induce polytomies.
lengths	Numeric vector of edge lengths, or a function that returns such a vector when passed the number of edges as its argument (e.g. runif).
addInTurn	Logical specifying whether to add leaves in the order of tips. If FALSE, leaves will be added in a random order.

Value

Each function returns an unweighted binary tree of class phylo with the specified leaf labels. Trees are rooted unless root = FALSE.

RandomTree() returns a topology drawn at random from the uniform distribution (i.e. each binary tree is drawn with equal probability). Trees are generated by inserting each tip in term at a randomly selected edge in the tree. Random numbers are generated using a Mersenne Twister. If root = FALSE, the tree will be unrooted, with the first tip in a basal position. Otherwise, the tree will be rooted on root.

YuleTree() returns a topology generated by the Yule process \insertCiteSteel2001TreeTools, i.e. adding leaves in turn adjacent to a randomly-chosen existing leaf.

PectinateTree() returns a pectinate (caterpillar) tree.

BalancedTree() returns a balanced (symmetrical) tree, in preorder.

StarTree() returns a completely unresolved (star) tree.

Author(s)

Martin R. Smith ([e-mail])

References

\insertAllCited

()

See Also

Other tree generation functions: ConstrainedNJ(), NJTree(), TreeNumber, TrivialTree

Examples

# Set random seed for reproducibility
set.seed(10)

# Generate a tree from a phylogenetic dataset
data("Lobo")
RandomTree(Lobo.phy, lengths = runif)

# Generate trees on letters A-J
plot(RandomTree(LETTERS[1:10], root = TRUE))

plot(YuleTree(LETTERS[1:10]))

plot(PectinateTree(LETTERS[1:10]))

plot(BalancedTree(LETTERS[1:10], lengths = 1:18))

plot(StarTree(LETTERS[1:10]))

TreeTools documentation built on June 2, 2026, 5:06 p.m.