Related papers: A One-to-One Correspondence between Natural Number…
Given a gene tree and a species tree, ancestral configurations represent the combinatorially distinct sets of gene lineages that can reach a given node of the species tree. They have been introduced as a data structure for use in the…
This paper proves that two differently defined rooted binary trees are isomorphic. The first tree is one associated to a version of Farey sequences where the vertices correspond to the open intervals formed by two successive terms in the…
In the paper are computed: the number of binary trees with n nodes and k leaves; the number of leaves in the set of all binary trees with n nodes. These are used to compute the number of states in the buddy system.
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…
Each natural number can be associated with some tree graph. Namely, a natural number $n$ can be factorized as $$ n = p_1^{\alpha_1}\ldots p_k^{\alpha_k},$$ where $p_i$ are distinct prime numbers. Since $\alpha_i$ are naturals, they can be…
Place value numbers, such as the binary or decimal numbers can be represented by the end vertices (leaf or pendant vertices) of rooted symmetrical trees. Numbers that consist of at most a fixed number of digits are represented by vertices…
Following Poupard's study of strictly ordered binary trees with respect to two parameters, namely, "end of minimal chain" and "parent of maximum leaf" a true Tree Calculus is being developed to solve a partial difference equation system and…
Tanglegrams are a special class of graphs appearing in applications concerning cospeciation and coevolution in biology and computer science. They are formed by identifying the leaves of two rooted binary trees. We give an explicit formula…
We study the random Fibonacci tree, which is an infinite binary tree with non-negative integers at each node. The root consists of the number 1 with a single child, also the number 1. We define the tree recursively in the following way: if…
In biology, a phylogenetic tree is a tool to represent the evolutionary relationship between species. Unfortunately, the classical Schr\"oder tree model is not adapted to take into account the chronology between the branching nodes. In…
We consider the enumeration of plane trees (rooted ordered trees) whose vertices are colored according to a specific coloring rule that prescribes which possible pairs of colors can occur as the colors of a parent vertex and its child. This…
We study some essential arithmetic properties of a new tree-based number representation, {\em hereditarily binary numbers}, defined by applying recursively run-length encoding of bijective base-2 digits. Our representation expresses giant…
Deciding whether there is a single tree -a supertree- that summarizes the evolutionary information in a collection of unrooted trees is a fundamental problem in phylogenetics. We consider two versions of this question: agreement and…
A new tree model is introduced based on ordered trees, by distinguishing exactly one child of each node that \emph{has} children. The basic enumeration leads to a cubic equation of the generating function. The extraction of its coefficients…
We study the sequences of numbers corresponding to lambda terms of given sizes, where the size is this of lambda terms with de Bruijn indices in a very natural model where all the operators have size 1. For plain lambda terms, the sequence…
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…
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 introduce a logical foundation to reason on tree structures with constraints on the number of node occurrences. Related formalisms are limited to express occurrence constraints on particular tree regions, as for instance the children of…
We present families of combinatorial classes described as trees with nodes that can carry one of two types of "flowers": integer partitions or integer compositions. Two parameters on the flowers of trees will be considered: the number of…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…