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This paper considers the enumeration of ternary trees (i.e. rooted ordered trees in which each vertex has 0 or 3 children) avoiding a contiguous ternary tree pattern. We begin by finding recurrence relations for several simple tree…

We define a bivariate polynomial for unlabeled rooted trees and show that the polynomial of an unlabeled rooted tree $T$ is the generating function of a class of subtrees of $T$. We prove that the polynomial is a complete isomorphism…

Tree shape statistics, particularly measures of tree (im)balance, play an important role in the analysis of the shape of phylogenetic trees. With applications ranging from testing evolutionary models to studying the impact of fertility…

We study a tree coloring model introduced by Guidon (2018), initially based on an analogy with a remote control system of a rail yard, seen as switches on a binary tree. For a given binary tree, we formalize the constraints on the coloring,…

The Yule process generates a class of binary trees which is fundamental to population genetic models and other applications in evolutionary biology. In this paper, we introduce a family of sub-classes of ranked trees, called Omega-trees,…

A partial order is called semilinear iff the upper bounds of each element are linearly ordered and any two elements have a common upper bound. There exists, up to isomorphism, a unique countable existentially closed semilinear order, which…

This is a survey article on trees, with a modest number of proofs to give a flavor of the way these topologies can be efficiently handled. Trees are defined in set-theorist fashion as partially ordered sets in which the elements below each…

Phylogenetic networks are a generalization of phylogenetic trees allowing for the representation of non-treelike evolutionary events such as hybridization. Typically, such networks have been analyzed based on their `level', i.e. based on…

Tree-based networks are a class of phylogenetic networks that attempt to formally capture what is meant by "tree-like" evolution. A given non-tree-based phylogenetic network, however, might appear to be very close to being tree-based, or…

Topological phylogenetic trees can be assigned edge weights in several natural ways, highlighting different aspects of the tree. Here the rooted triple and quartet metrizations are introduced, and applied to formulate novel fast methods of…

We propose a new arithmetic for non-empty rooted unordered trees simply called trees. After discussing tree representation and enumeration, we define the operations of tree addition, multiplication and stretch, prove their properties, and…

We study the influence of the seed in random trees grown according to the uniform attachment model, also known as uniform random recursive trees. We show that different seeds lead to different distributions of limiting trees from a total…

A closed-form formula is derived for the number of occurrences of matches of a multiset of patterns among all ordered (plane-planted) trees with a given number of edges. A pattern looks like a tree, with internal nodes and leaves, but also…

We show that a tree of order $n$ has at most $O(5^{n/4})$ nonisomorphic subtrees, and that this bound is best possible. We also prove an analogous result for the number of nonisomorphic rooted subtrees of a rooted tree.

Null models of binary phylogenetic trees are useful for testing hypotheses on real world phylogenies. In this paper we consider phylogenies as binary trees without edge lengths together with a sampling measure and encode them as algebraic…

Some posets of binary leaf-labeled trees are shown to be supersolvable lattices and explicit EL-labelings are given. Their characteristic polynomials are computed, recovering their known factorization in a different way.

We propose the first branch-&-price algorithm for the maximum agreement forest problem on unrooted binary trees: given two unrooted X-labelled binary trees we seek to partition X into a minimum number of blocks such that the induced…

Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…

Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly…

Sorting is a foundational problem in computer science that is typically employed on sequences or total orders. More recently, a more general form of sorting on partially ordered sets (or posets), where some pairs of elements are…