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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…
Phylogenetic networks are a type of leaf-labelled, acyclic, directed graph used by biologists to represent the evolutionary history of species whose past includes reticulation events. A phylogenetic network is tree-child if each non-leaf…
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…
A rooted phylogenetic network is a directed acyclic graph with a single root, whose sinks correspond to a set of species. As such networks are useful for representing the evolution of species that have undergone reticulate evolution, there…
A connectivity function on a finite set $V$ is a symmetric submodular function $f \colon 2^V \to \mathbb{Z}$ with $f(\emptyset)=0$. We prove that finding a branch-decomposition of width at most $k$ for a connectivity function given by an…
In evolutionary biology, networks are becoming increasingly used to represent evolutionary histories for species that have undergone non-treelike or reticulate evolution. Such networks are essentially directed acyclic graphs with a leaf set…
We consider the following basic problem in phylogenetic tree construction. Let $\mathcal{P} = \{T_1, \ldots, T_k\}$ be a collection of rooted phylogenetic trees over various subsets of a set of species. The tree compatibility problem asks…
Vertex deletion and edge deletion problems play a central role in Parameterized Complexity. Examples include classical problems like Feedback Vertex Set, Odd Cycle Transversal, and Chordal Deletion. Interestingly, the study of edge…
Orthology and paralogy relations are often inferred by methods based on gene similarity, which usually yield a graph depicting the relationships between gene pairs. Such relation graphs are known to frequently contain errors, as they cannot…
Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…
Let $\mathcal{D}$ be a set family that is the solution domain of some combinatorial problem. The \emph{max-min diversification problem on $\mathcal{D}$} is the problem to select $k$ sets from $\mathcal{D}$ such that the Hamming distance…
Fixed-parameter tractability analysis and scheduling are two core domains of combinatorial optimization which led to deep understanding of many important algorithmic questions. However, even though fixed-parameter algorithms are appealing…
For many taxa, the current high rates of extinction are likely to result in a significant loss of biodiversity. The evolutionary heritage of biodiversity is frequently quantified by a measure called phylogenetic diversity (PD). We predict…
In $d$-Scattered Set we are given an (edge-weighted) graph and are asked to select at least $k$ vertices, so that the distance between any pair is at least $d$, thus generalizing Independent Set. We provide upper and lower bounds on the…
It has remained an open question for some time whether, given a set of not necessarily binary (i.e. "nonbinary") trees T on a set of taxa X, it is possible to determine in time f(r).poly(m) whether there exists a phylogenetic network that…
Fixed tree topologies are widely used in phylodynamic analyses to reduce computational burden, yet the consequences of this assumption remain insufficiently understood. Here, we systematically assess the impact of various fixed-topology…
In the vertex connectivity augmentation problem, we are given an undirected $n$-vertex graph $G$, a set of links $L \subseteq \binom{V(G)}{2} \setminus E(G)$, and integers $\lambda$ and $k$. The task is to insert at most $k$ links from $L$…
We study the parameterized complexity of the classical Edge Hamiltonian Path problem and give several fixed-parameter tractability results. First, we settle an open question of Demaine et al. by showing that Edge Hamiltonian Path is FPT…
In this paper, we present fixed-parameter tractability algorithms for both the undirected and directed versions of the Spanning Tree Isomorphism Problem, parameterized by the size $k$ of a redundant set. A redundant set is a collection of…
Parameterized complexity seeks to use input structure to obtain faster algorithms for NP-hard problems. This has been most successful for graphs of low treewidth: Many problems admit fast algorithms relative to treewidth and many of them…