Bioinformatics regularly poses new challenges to algorithm engineers and theoretical
computer scientists. This work surveys recent developments of parameterized algorithms …

Given a rooted, binary phylogenetic network and a rooted, binary phylogenetic tree, can the
tree be embedded into the network? This problem, called TREE CONTAINMENT, arises …

We consider the NP-hard Tree Containment problem that has important applications in
phylogenetics. The problem asks if a given single-rooted leaf-labeled network …

Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed
phylogenetic network, representing the evolutionary history of certain species. Tree …

Phylogenetic networks are a type of graph with vertices and edges, used to elucidate the
evolutionary history of species. The fundamental goal of phylogenetic research is to infer the …

Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently
showed that the problem of deciding if two phylogenetic networks embed the same sets of …

Phylogenetic trees are unable to represent the evolutionary process for a collection of
species if reticulation events happened, and a generalized model named phylogenetic …

This thesis presents faster (in terms of worst-case running times) exact algorithms for special
cases of graph problems through dynamic programming and 2-SAT programming. Dynamic …

Abstract The ${\rm T {\small REE}~ C {\small ONTAINMENT}} $ problem has many important
applications in the study of evolutionary history. Given a phylogenetic network $ N $ and a …

Galled trees are studied as a recombination model in theoretical population genetics. Tree-
child networks, reticulation-visible networks and tree-based networks can be considered as …