Related papers: Reconstructing phylogenetic level-1 networks from …
Rooted phylogenetic networks are used by biologists to infer and represent complex evolutionary relationships between species that cannot be accurately explained by a phylogenetic tree. Tree-child networks are a particular class of rooted…
Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…
Horizontal gene transfer (HGT) is an important process in bacterial evolution. Current phylogeny-based approaches to capture it cannot however appropriately account for the fact that HGT can occur between bacteria living in different…
We propose a method combining boundary integral equations and neural networks (BINet) to solve partial differential equations (PDEs) in both bounded and unbounded domains. Unlike existing solutions that directly operate over original PDEs,…
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent reticulate evolution. Unrooted phylogenetic networks form a special class of such networks, which naturally generalize unrooted phylogenetic trees.…
Network topology plays a key role in many phenomena, from the spreading of diseases to that of financial crises. Whenever the whole structure of a network is unknown, one must resort to reconstruction methods that identify the least biased…
We present an algorithm for phylogenetic reconstruction using quartets that returns the correct topology for $n$ taxa in $O(n \log n)$ time with high probability, in a probabilistic model where a quartet is not consistent with the true…
It has recently been shown that the NP-hard problem of calculating the minimum number of hybridization events that is needed to explain a set of rooted binary phylogenetic trees by means of a hybridization network is fixed-parameter…
A tree-based network $N$ on $X$ is called universal if every phylogenetic tree on $X$ is a base tree for $N$. Recently, binary universal tree-based networks have attracted great attention in the literature and their existence has been…
In evolutionary biology, phylogenetic trees are commonly inferred from a set of characters (partitions) of a collection of biological entities (e.g., species or individuals in a population). Such characters naturally arise from molecular…
Phylogenetic trees are widely used to display estimates of how groups of species evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees…
Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…
We show that many topological features of level-1 species networks are identifiable from the distribution of the gene tree quartets under the network multi-species coalescent model. In particular, every cycle of size at least 4 and every…
A challenging problem in complex networks is the network reconstruction problem from data. This work deals with a class of networks denoted as conserved networks, in which a flow associated with every edge and the flows are conserved at all…
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…
Interest in the inference of evolutionary networks relating species or populations has grown with the increasing recognition of the importance of hybridization, gene flow and admixture, and the availability of large-scale genomic data.…
We consider the problems of computing maximal palindromes and distinct palindromes in a trie. A trie is a natural generalization of a string, which can be seen as a single-path tree. There is a linear-time offline algorithm to compute…
In evolutionary biology, phylogenetic networks are graphs that provide a flexible framework for representing complex evolutionary histories that involve reticulate evolutionary events. Recently phylogenetic studies have started to focus on…
Natural and man-made transport webs are frequently dominated by dense sets of nested cycles. The architecture of these networks, as defined by the topology and edge weights, determines how efficiently the networks perform their function.…
It is known that any two trees on the same $n$ leaves can be displayed by a network with $n-2$ reticulations, and there are two trees that cannot be displayed by a network with fewer reticulations. But how many reticulations are needed to…