Related papers: Two metrics for general phylogenetic networks

The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately…

We demonstrate the use of computational phylogenetic techniques to solve a central problem in inferential network monitoring. More precisely, we design a novel algorithm for multicast-based delay inference, i.e. the problem of…

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…

Here we show that deciding whether two rooted binary phylogenetic trees on the same set of taxa permit a cherry-picking sequence, a special type of elimination order on the taxa, is NP-complete. This improves on an earlier result which…

Phylogenetic networks play an important role in evolutionary biology as, other than phylogenetic trees, they can be used to accommodate reticulate evolutionary events such as horizontal gene transfer and hybridization. Recent research has…

In this paper, we study approximation properties of single hidden layer neural networks with weights varying on finitely many directions and thresholds from an open interval. We obtain a necessary and at the same time sufficient measure…

Phylogenetic networks provide a way to describe and visualize evolutionary histories that have undergone so-called reticulate evolutionary events such as recombination, hybridization or horizontal gene transfer. The level k of a network…

We address the question of finding the community structure of a complex network. In an earlier effort [H. Zhou, {\em Phys. Rev. E} (2003)], the concept of network random walking is introduced and a distance measure defined. Here we…

We provide a general framework for analyzing degree correlations between nodes separated by more than one step (i.e., beyond nearest neighbors) in complex networks. One probability and four conditional probabilities are introduced to fully…

Network data is a major object data type that has been widely collected or derived from common sources such as brain imaging. Such data contains numeric, topological, and geometrical information, and may be necessarily considered in certain…

We study the genealogical distance of two randomly chosen individuals in a population that evolves according to a two type Moran model with mutation and selection. We prove that this distance is stochastically smaller than the corresponding…

Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…

We introduce a scale-free method for testing the proportionality of branch lengths between two phylogenetic trees that have the same topology and contain the same set of taxa. This method scales both trees to a total length of 1 and sums up…

Measure the similarity of the nodes in the complex networks have interested many researchers to explore it. In this paper, a new method which is based on the degree centrality and the Relative-entropy is proposed to measure the similarity…

In a previous work, we gave a metric on the class of semibinary tree-sibling time consistent phylogenetic networks that is computable in polynomial time; in particular, the problem of deciding if two networks of this kind are isomorphic is…

In large networks, using the length of shortest paths as the distance measure has shortcomings. A well-studied shortcoming is that extending it to disconnected graphs and directed graphs is controversial. The second shortcoming is that a…

Phylogenetic trees are often constructed by using a metric on the set of taxa that label the leaves of the tree. While there are a number of methods for constructing a tree using a given metric, such trees will only display the metric if it…

Phylogenetic networks are a special type of graph which generalize phylogenetic trees and that are used to model non-treelike evolutionary processes such as recombination and hybridization. In this paper, we consider {\em unrooted}…

Hybrid evolution and horizontal gene transfer (HGT) are processes where evolutionary relationships may more accurately be described by a reticulated network than by a tree. In such a network, there will often be several paths between any…

Phylogenetic networks can represent evolutionary events that cannot be described by phylogenetic trees. These networks are able to incorporate reticulate evolutionary events such as hybridization, introgression, and lateral gene transfer.…