Related papers: Constructing a Minimum-Level Phylogenetic Network …
The need for structures capable of accommodating complex evolutionary signals such as those found in, for example, wheat has fueled research into phylogenetic networks. Such structures generalize the standard phylogenetic tree model by also…
We consider problems that can be formulated as a task of finding an optimal triangulation of a graph w.r.t. some notion of optimality. We present algorithms parameterized by the size of a minimum edge clique cover ($cc$) to such problems.…
Quartet Reconstruction, the task of recovering a phylogenetic tree from smaller trees on four species called \textit{quartets}, is a well-studied problem in theoretical computer science with far-reaching connections to statistics, graph…
Compatibility of unrooted phylogenetic trees is a well studied problem in phylogenetics. It asks to determine whether for a set of k input trees there exists a larger tree (called a supertree) that contains the topologies of all k input…
In comparison to phylogenetic trees, phylogenetic networks are more suitable to represent complex evolutionary histories of species whose past includes reticulation such as hybridisation or lateral gene transfer. However, the reconstruction…
Galled trees are studied as a recombination model in theoretic population genetics. This class of phylogenetic networks has been generalized to tree-child networks, normal networks and tree-based networks by relaxing a structural condition.…
Different sources of information might tell different stories about the evolutionary history of a given set of species. This leads to (rooted) phylogenetic trees that "disagree" on triples of species, which we call "conflict triples". An…
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…
A contemporary and fundamental problem faced by many evolutionary biologists is how to puzzle together a collection $\mathcal P$ of partial trees (leaf-labelled trees whose leaves are bijectively labelled by species or, more generally,…
Genetic and comparative genomic studies indicate that extant genomes are more properly considered to be a fusion product of random mutations over generations and genomic material transfers between individuals of different lineages. This has…
Characterization of joint probability distribution for large networks of random variables remains a challenging task in data science. Probabilistic graph approximation with simple topologies has practically been resorted to; typically 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…
We systematically study the computational complexity of a broad class of computational problems in phylogenetic reconstruction. The class contains for example the rooted triple consistency problem, forbidden subtree problems, the quartet…
Phylogenetic networks are used to represent evolutionary scenarios in biology and linguistics. To find the most probable scenario, it may be necessary to compare candidate networks, to distinguish different networks, and to see when one…
Phylogenetic networks generalize phylogenetic trees by allowing reticulate evolutionary events such as horizontal gene transfer and hybridization. Among the many subclasses of phylogenetic networks, orchard networks have attracted…
Phylogenetic networks provide a more general description of evolutionary relationships than rooted phylogenetic trees. One way to produce a phylogenetic network is to randomly place $k$ arcs between the edges of a rooted binary phylogenetic…
In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…
Phylogenetic networks are graphs that are used to represent evolutionary relationships between different taxa. They generalize phylogenetic trees since for example, unlike trees, they permit lineages to combine. Recently, there has been…
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)…
In the Maximize Phylogenetic Diversity problem, we are given a phylogenetic tree that represents the genetic proximity of species, and we are asked to select a subset of species of maximum phylogenetic diversity to be preserved through…