Related papers: Finding Maximum Common Contractions Between Phylog…
The presence of reticulate evolutionary events in phylogenies turn phylogenetic trees into phylogenetic networks. These events imply in particular that there may exist multiple evolutionary paths from a non-extant species to an extant one,…
Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…
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,…
The problem of reconstructing evolutionary trees or phylogenies is of great interest in computational biology. A popular model for this problem assumes that we are given the set of leaves (current species) of an unknown binary tree and the…
High order networks are weighted hypergraphs col- lecting relationships between elements of tuples, not necessarily pairs. Valid metric distances between high order networks have been defined but they are difficult to compute when the…
Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…
We consider the problem of optimally compressing and caching data across a communication network. Given the data generated at edge nodes and a routing path, our goal is to determine the optimal data compression ratios and caching decisions…
Tree-based networks are a class of phylogenetic networks that attempt to formally capture what is meant by "tree-like" evolution. A given non-tree-based phylogenetic network, however, might appear to be very close to being tree-based, or…
An important and well-studied problem in phylogenetics is to compute a \emph{consensus tree} so as to summarize the common features within a collection of rooted phylogenetic trees, all whose leaf-sets are bijectively labeled by the same…
Finding a maximum clique in a given graph is one of the fundamental NP-hard problems. We compare two multi-core thread-parallel adaptations of a state-of-the-art branch and bound algorithm for the maximum clique problem, and provide a novel…
We introduce a new phylogenetic reconstruction algorithm which, unlike most previous rigorous inference techniques, does not rely on assumptions regarding the branch lengths or the depth of the tree. The algorithm returns a forest which is…
Compression and sparsification algorithms are frequently applied in a preprocessing step before analyzing or optimizing large networks/graphs. In this paper we propose and study a new framework contracting edges of a graph (merging vertices…
In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In…
Phylogenetic networks are a flexible model of evolution that can represent reticulate evolution and handle complex data. Tree-based networks, which are phylogenetic networks that have a spanning tree with the same root and leaf-set as the…
It is required to find an optimal order of constructing the edges of a network so as to minimize the sum of the weighted connection times of relevant pairs of vertices. Construction can be performed anytime anywhere in the network, with a…
Phylogenetic networks generalize phylogenetic trees in order to model reticulation events. Although the comparison of phylogenetic trees is well studied, and there are multiple ways to do it in an efficient way, the situation is much…
The mutational heterogeneity of tumours can be described with a tree representing the evolutionary history of the tumour. With noisy sequencing data there may be uncertainty in the inferred tree structure, while we may also wish to study…
An evolutionary tree is a rooted tree where each internal vertex has at least two children and where the leaves are labeled with distinct symbols representing species. Evolutionary trees are useful for modeling the evolutionary history of…
Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains…
We describe a kernel of size 9k-8 for the NP-hard problem of computing the Tree Bisection and Reconnect (TBR) distance k between two unrooted binary phylogenetic trees. We achieve this by extending the existing portfolio of reduction rules…