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Phylogenetic networks are increasingly being considered as better suited to represent the complexity of the evolutionary relationships between species. One class of phylogenetic networks that has received a lot of attention recently is the…
Dual-tree algorithms are a widely used class of branch-and-bound algorithms. Unfortunately, developing dual-tree algorithms for use with different trees and problems is often complex and burdensome. We introduce a four-part logical split:…
This paper introduces constNJ, the first algorithm for phylogenetic reconstruction of sets of trees with constrained pairwise rooted subtree-prune regraft (rSPR) distance. We are motivated by the problem of constructing sets of trees which…
A variety of algorithms have been proposed for reconstructing trees that show the evolutionary relationships between species by comparing differences in genetic data across present-day taxa. If the leaf-to-leaf distances in a tree can be…
A tree decomposition of the coordinates of a code is a mapping from the coordinate set to the set of vertices of a tree. A tree decomposition can be extended to a tree realization, i.e., a cycle-free realization of the code on the…
Popular methods for exploring the space of rooted phylogenetic trees use rearrangement moves such as rNNI (rooted Nearest Neighbour Interchange) and rSPR (rooted Subtree Prune and Regraft). Recently, these moves were generalized to rooted…
In molecular systematics, evolutionary trees are reconstructed from sequences at the tips under simple models of site substitution. A central question is how much sequence data is required to reconstruct a tree accurately? The answer…
In this letter we show how to improve the performance of backward chained behavior trees (BTs) that use reinforcement learning (RL). BTs represent a hierarchical and modular way of combining control policies into higher level control…
The rank (also known as protection number or leaf-height) of a vertex in a rooted tree is the minimum distance between the vertex and any of its leaf descendants. We consider the sum of ranks over all vertices (known as the security) in…
We present sublinear-time (randomized) algorithms for finding simple cycles of length at least $k\geq 3$ and tree-minors in bounded-degree graphs. The complexity of these algorithms is related to the distance of the graph from being…
In the usual trace reconstruction problem, the goal is to exactly reconstruct an unknown string of length $n$ after it passes through a deletion channel many times independently, producing a set of traces (i.e., random subsequences of the…
In this paper, we consider a tree inference problem motivated by the critical problem in single-cell genomics of reconstructing dynamic cellular processes from sequencing data. In particular, given a population of cells sampled from such a…
Orchard and tree-child networks share an important property with phylogenetic trees: they can be completely reduced to a single node by iteratively deleting cherries and reticulated cherries. As it is the case with phylogenetic trees, the…
The decycling number of a graph $G$ is the minimum number of vertices whose removal from $G$ results in an acyclic subgraph. It is known that determining the decycling number of a graph $G$ is equivalent to finding the maximum induced…
Phylogenetic trees are used to model evolution: leaves are labelled to represent contemporary species ("taxa") and interior vertices represent extinct ancestors. Informally, convex characters are measurements on the contemporary species in…
We study the number of distance queries needed to identify certain properties of a hidden tree $T$ on $n$ vertices. A distance query consists of two vertices $x,y$, and the answer is the distance of $x$ and $y$ in $T$. We determine the…
A central theme in phylogenetics is the reconstruction and analysis of evolutionary trees from a given set of data. To determine the optimal search methods for reconstructing trees, it is crucial to understand the size and structure of the…
Rooted phylogenetic networks are often constructed by combining trees, clusters, triplets or characters into a single network that in some well-defined sense simultaneously represents them all. We review these four models and investigate…
We define the (random) $k$-cut number of a rooted graph to model the difficulty of the destruction of a resilient network. The process is as the cut model of Meir and Moon except now a node must be cut $k$ times before it is destroyed. The…
A promising approach for obtaining improved approximation algorithms for Steiner tree is to use the bidirected cut relaxation (BCR). The integrality gap of this relaxation is at least $36/31$, and it has long been conjectured that its true…