Related papers: Incomplete Directed Perfect Phylogeny in Linear Ti…
The binary perfect phylogeny model is too restrictive to model biological events such as back mutations. In this paper we consider a natural generalization of the model that allows a special type of back mutation. We investigate the problem…
We study a character-based phylogeny reconstruction problem when an incomplete set of data is given. More specifically, we consider the situation under the directed perfect phylogeny assumption with binary characters in which for some…
The perfect phylogeny is one of the most used models in different areas of computational biology. In this paper we consider the problem of the Persistent Perfect Phylogeny (referred as P-PP) recently introduced to extend the perfect…
The Persistent Perfect phylogeny, also known as Dollo-1, has been introduced as a generalization of the well-known perfect phylogenetic model for binary characters to deal with the potential loss of characters. The problem of deciding the…
The Dollo model for reconstructing evolutionary trees from binary characters has been proposed as a generalization of the infinite sites model, also known as the Perfect Phylogeny. In particular, the Dollo model is considered more realistic…
Depth first search (DFS) tree is a fundamental data structure for solving graph problems. The classical algorithm [SiComp74] for building a DFS tree requires $O(m+n)$ time for a given graph $G$ having $n$ vertices and $m$ edges. Recently,…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
We study the problem of constructing phylogenetic trees for a given set of species. The problem is formulated as that of finding a minimum Steiner tree on $n$ points over the Boolean hypercube of dimension $d$. It is known that an optimal…
Haplotyping is the bioinformatics problem of predicting likely haplotypes based on given genotypes. It can be approached using Gusfield's perfect phylogeny haplotyping (PPH) method for which polynomial and linear time algorithms exist.…
The Persistent-Phylogeny Model is an extension of the widely studied Perfect-Phylogeny Model, encompassing a broader range of evolutionary phenomena. Biological and algorithmic questions concerning persistent phylogeny have been intensely…
Kloks, Kratsch, and Spinrad showed how treewidth and minimum-fill, NP-hard combinatorial optimization problems related to minimal triangulations, are broken into subproblems by block subgraphs defined by minimal separators. These ideas were…
In a graph, a (perfect) matching cut is an edge cut that is a (perfect) matching. Matching Cut (MC), respectively, Perfect Matching Cut (PMC), is the problem of deciding whether a given graph has a matching cut, respectively, a perfect…
The three-in-a-tree problem is to determine if a simple undirected graph contains an induced subgraph which is a tree connecting three given vertices. Based on a beautiful characterization that is proved in more than twenty pages,…
We show that the problem of constructing tree-structured descriptions of data layouts that are optimal with respect to space or other criteria from given sequences of displacements, can be solved in polynomial time. The problem is relevant…
Storyline drawings are a popular visualization of interactions of a set of characters over time, e.g., to show participants of scenes in a book or movie. Characters are represented as $x$-monotone curves that converge vertically for…
The reconstruction of the history of evolutionary genome-wide events among a set of related organisms is of great biological interest. A simplified model that captures only content modifying operations was introduced recently. It allows the…
Deriving relationships between images and tracing back their history of modifications are at the core of Multimedia Phylogeny solutions, which aim to combat misinformation through doctored visual media. Nonetheless, most recent image…
Attempting to recognize a tree inside a phylogenetic network is a fundamental undertaking in evolutionary analysis. In the last few years, therefore, tree-based phylogenetic networks, which are defined by a spanning tree called a…
Predicting horizontal gene transfers often requires comparative sequence data, but recent work has shown that character-based approaches could also be useful for this task. Notably, perfect transfer networks (PTN) explain the character…
We revisit the vertex-failure connectivity oracle problem. This is one of the most basic graph data structure problems under vertex updates, yet its complexity is still not well-understood. We essentially settle the complexity of this…