Related papers: On the existence of a cherry-picking sequence
Given two rooted, ordered, and labeled trees $P$ and $T$ the tree inclusion problem is to determine if $P$ can be obtained from $T$ by deleting nodes in $T$. This problem has recently been recognized as an important query primitive in XML…
An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
Rooted phylogenetic networks provide a more complete representation of the ancestral relationship between species than phylogenetic trees when reticulate evolutionary processes are at play. One way to reconstruct a phylogenetic network is…
Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…
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 $X$…
Network Phylogenetic Diversity (Network-PD) is a measure for the diversity of a set of species based on a rooted phylogenetic network (with branch lengths and inheritance probabilities on the reticulation edges) describing the evolution of…
Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral…
Consider any locally checkable labeling problem $\Pi$ in rooted regular trees: there is a finite set of labels $\Sigma$, and for each label $x \in \Sigma$ we specify what are permitted label combinations of the children for an internal node…
An important problem in phylogenetics is the construction of phylogenetic trees. One way to approach this problem, known as the supertree method, involves inferring a phylogenetic tree with leaves consisting of a set $X$ of species from a…
Frequent tree mining asks us to enumerate tree patterns that occur frequently in a database of rooted trees. This problem is motivated by tree-structured data in bioinformatics, such as glycans and pseudoknot-free RNA secondary structures.…
The recursive and hierarchical structure of full rooted trees is applicable to represent statistical models in various areas, such as data compression, image processing, and machine learning. In most of these cases, the full rooted tree is…
Phylogenetic networks are a generalization of evolutionary trees that are used by biologists to represent the evolution of organisms which have undergone reticulate evolution. Essentially, a phylogenetic network is a directed acyclic graph…
Graph pebbling is a network model for transporting discrete resources that are consumed in transit. Deciding whether a given configuration on a particular graph can reach a specified target is ${\sf NP}$-complete, even for diameter two…
Invariants for complicated objects such as those arising in phylogenetics, whether they are invariants as matrices, polynomials, or other mathematical structures, are important tools for distinguishing and working with such objects. In this…
Here we present a new fixed parameter tractable algorithm to compute the hybridization number r of two rooted, not necessarily binary phylogenetic trees on taxon set X in time (6^r.r!).poly(n)$, where n=|X|. The novelty of this approach is…
In this paper, we study the parallel query complexity of reconstructing biological and digital phylogenetic trees from simple queries involving their nodes. This is motivated from computational biology, data protection, and computer…
We compare the phylogenetic tensors for various trees and networks for two, three and four taxa. If the probability spaces between one tree or network and another are not identical then there will be phylogenetic tensors that could have…
We consider the following generalization of binary search in sorted arrays to tree domains. In each step of the search, an algorithm is querying a vertex $q$, and as a reply, it receives an answer, which either states that $q$ is the…
In the study of rooted phylogenetic networks, analyzing the set of rooted phylogenetic trees that are embedded in such a network is a recurring task. From an algorithmic viewpoint, this analysis almost always requires an exhaustive search…