Related papers: Combinatorics of pedigrees
We investigate the structure and reconstruction complexity of Manacher arrays. First, we establish a combinatorial lower bound, proving that the number of rooted tandem repeat trees with $n+1$ genes exceeds the number of distinct Manacher…
Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene…
Phylogenetic network is an evolutionary model that uses a rooted directed acyclic graph (instead of a tree) to model an evolutionary history of species in which reticulate events (e.g., hybrid speciation or horizontal gene transfer)…
A dominating set of a graph is a set of vertices such that every vertex not in the set has at least one neighbor in the set. The problem of counting dominating sets is #P-complete for chordal graphs but solvable in polynomial time for its…
Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…
We introduce a new model of indeterminacy in graphs: instead of specifying all the edges of the graph, the input contains all triples of vertices that form a connected subgraph. In general, different (labelled) graphs may have the same set…
Distance-hereditary graphs form an important class of graphs, from the theoretical point of view, due to the fact that they are the totally decomposable graphs for the split-decomposition. The previous best enumerative result for these…
We investigate structural and algorithmic advantages of a directed version of the well-researched class of distance-hereditary graphs. Since the previously defined distance-hereditary digraphs do not permit a recursive structure, we define…
Tree-child networks are a recently-described class of directed acyclic graphs that have risen to prominence in phylogenetics (the study of evolutionary trees and networks). Although these networks have a number of attractive mathematical…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
Unrooted phylogenetic networks are graphs used to represent evolutionary relationships. Accurately reconstructing such networks is of great relevance for evolutionary biology. It has recently been conjectured that all phylogenetic networks…
Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…
Motivation: Millions of genes in the modern species belong to only thousands of `gene families'. A gene family includes instances of the same gene in different species (orthologs) and duplicate genes in the same species (paralogs). Genes…
Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary…
Working with generating functions, the combinatorics of a recurrence relation can be expressed in a way that allows for more efficient calculation of the quantity. This is true of the Catalan numbers for an ordered binary tree…
In this paper, we introduce a class of graphs which we call average hereditary graphs. Many graphs that occur in the usual graph theory applications belong to this class of graphs. Many popular types of graphs fall under this class, such as…
Given a set of species whose evolution is represented by a species tree, a gene family is a group of genes having evolved from a single ancestral gene. A gene family evolves along the branches of a species tree through various mechanisms,…
We study an abstract notion of tree structure which lies at the common core of various tree-like discrete structures commonly used in combinatorics: trees in graphs, order trees, nested subsets of a set, tree-decompositions of graphs and…
This survey article is devoted to general results in combinatorial enumeration. The first part surveys results on growth of hereditary properties of combinatorial structures. These include permutations, ordered and unordered graphs and…
Graphlets are subgraphs rooted at a fixed vertex. The number of occurrences of graphlets aligned to a particular vertex, called graphlet degree sequence (gds), gives a topological description of the surrounding of the analyzed vertex.…