Related papers: Non-well-founded trees in categories
We formalize an existing computability-theoretic method of presenting first-order structures whose domains have the cardinality of the continuum. Work using these methods until now has emphasized their topological properties. We shift the…
$\omega$-clones are multi-sorted structures that naturally emerge as algebras for infinite trees, just as $\omega$-semigroups are convenient algebras for infinite words. In the algebraic theory of languages, one hopes that a language is…
We study varieties that contain unranked tree languages over all alphabets. Trees are labeled with symbols from two alphabets, an unranked operator alphabet and an alphabet used for leaves only. Syntactic algebras of unranked tree languages…
We construct recursion categories from categories of coalgebras. Let $F$ be a nontrivial endofunctor on the category of sets that weakly preserves pullbacks and such that the category $\textbf{Set}_F$ of $F$-coalgebras is complete. The…
Generalized trees, we call them O-trees, are defined as hierarchical partial orders, i.e., such that the elements larger than any one are linearly ordered. Quasi-trees are, roughly speaking, undirected O-trees. For O-trees and quasi-trees,…
Within dependent type theory, we provide a topological counterpart of well-founded trees (for short, W-types) by using a proof-relevant version of the notion of inductively generated suplattices introduced in the context of formal topology…
Logic languages based on the theory of rational, possibly infinite, trees have much appeal in that rational trees allow for faster unification (due to the safe omission of the occurs-check) and increased expressivity (cyclic terms can…
In evolutionary biology, networks are becoming increasingly used to represent evolutionary histories for species that have undergone non-treelike or reticulate evolution. Such networks are essentially directed acyclic graphs with a leaf set…
Trees fill many extremal roles in graph theory, being minimally connected and serving a critical role in the definition of $n$-good graphs. In this article, we consider the generalization of trees to the setting of $r$-uniform hypergraphs…
Any algebraic connection on a vector bundle on a smooth complex algebraic curve determines an irregular class and in turn a fission tree at each puncture. The fission trees are the discrete data classifying the admissible deformation…
We compare three basic kinds of discrete mathematical models used to portray phylogenetic relationships among species and higher taxa: phylogenetic trees, Hennig trees and Nelson cladograms. All three models are trees, as that term is…
A tree-based network $N$ on $X$ is called universal if every phylogenetic tree on $X$ is a base tree for $N$. Recently, binary universal tree-based networks have attracted great attention in the literature and their existence has been…
Tree sets are posets with additional structure that generalize tree-like objects in graphs, matroids, or other combinatorial structures. They are a special class of abstract separation systems. We study infinite tree sets and how they…
Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic…
Tree-width is an invaluable tool for computational problems on graphs. But often one would like to compute on other kinds of objects (e.g. decorated graphs or even algebraic structures) where there is no known tree-width analogue. Here we…
The theory of {\Gamma}-species is developed to allow species-theoretic study of quotient structures in a categorically rigorous fashion. This new approach is then applied to two graph-enumeration problems which were previously unsolved in…
One of the goals of phylogenetic research is to find the species tree describing the evolutionary history of a set of species. But the trees derived from geneti data with the help of tree inference methods are gene trees that need not…
We construct tree-decompositions of graphs that distinguish all their k-blocks and tangles of order k, for any fixed integer k. We describe a family of algorithms to construct such decompositions, seeking to maximize their diversity subject…
Trees or rooted trees have been generously studied in the literature. A forest is a set of trees or rooted trees. Here we give recurrence relations between the number of some kind of rooted forest with $k$ roots and that with $k+1$ roots on…
Combinatorial objects such as rooted trees that carry a recursive structure have found important applications recently in both mathematics and physics. We put such structures in an algebraic framework of operated semigroups. This framework…