Related papers: Seven Trees in One
A normal network is uniquely determined by the set of phylogenetic trees that it displays. Given a set $\mathcal{P}$ of rooted binary phylogenetic trees, this paper presents a polynomial-time algorithm that reconstructs the unique binary…
The reconstruction of a central tendency `species tree' from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all…
Tree sets are abstract structures that can be used to model various tree-shaped objects in combinatorics. Finite tree sets can be represented by finite graph-theoretical trees. We extend this representation theory to infinite tree sets.…
Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…
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 develop a notion of a dual of a graph, generalizing the definition of Goulden and Yong (which only applied to trees), and reproving their main result using our new notion. We in fact give three definitions of the dual: a graph-theoretic…
A function on an algebra is congruence preserving if, for any congruence, it maps pairs of congruent elements onto pairs of congruent elements. We show that on the algebra of complete binary trees whose leaves are labeled by letters of an…
In this paper, we construct a seven-term exact sequence involving the cohomology groups of a group extension. Although the existence of such a sequence can be derived using spectral sequence arguments, there is little knowledge about some…
The ternary relation $B(x,y,z)$ of betweenness states that an element $y$ is between the elements $x$ and $z$, in some sense depending on the considered structure. In a partially ordered set $(N,\leq)$, $B(x,y,z):\Longleftrightarrow…
We prove that for any finite tree $T$ with $n$ vertices and maximal degree $3$, there is a topological embedding of $T$ into the integer grid $Z^2$ which maps vertices to vertices and whose image meets at most $\frac{7}{3}n$ vertices. This…
The Subtree Isomorphism problem asks whether a given tree is contained in another given tree. The problem is of fundamental importance and has been studied since the 1960s. For some variants, e.g., ordered trees, near-linear time algorithms…
Species trees represent the historical divergences of populations or species, while gene trees trace the ancestry of individual gene copies sampled within those populations. In cases involving rapid speciation, gene trees with topologies…
We consider the decentralized binary hypothesis testing problem on trees of bounded degree and increasing depth. For a regular tree of depth t and branching factor k>=2, we assume that the leaves have access to independent and identically…
In an award-winning expository article, V. Pozdnyakov and J.M. Steele gave a beautiful demonstration of the ramifications of a basic bijection for permutations. The aim of this note is to connect this correspondence to a seemingly unrelated…
We present a general bijective approach to planar hypermaps with two main results. First we obtain unified bijections for all classes of maps or hypermaps defined by face-degree constraints and girth constraints. To any such class we…
Among other results, we prove the following theorem about Steiner minimal trees in $d$-dimensional Euclidean space: if two finite sets in $\mathbb{R}^d$ have unique and combinatorially equivalent Steiner minimal trees, then there is a…
Set partitions avoiding $k$-crossing and $k$-nesting have been extensively studied from the aspects of both combinatorics and mathematical biology. By using the generating tree technique, the obstinate kernel method and Zeilberger's…
We introduce essential subtrees for terms (trees) and tree automata . There are some results concerning independent sets of subtrees and separable sets for a tree and an automaton.
We examine clusters in the cluster tube of rank $n+1$ using exceptional sequences in the abelian tube of rank $n+1$. Although the abelian tube has more exceptional sequences than the module categories of type $B_{n}/C_{n}$, we obtain a…
The purpose of this article is to show how the isotropy subgroup of leaf permutations on binary trees can be used to systematically identify tree-informative invariants relevant to models of phylogenetic evolution. In the quartet case, we…