相关论文: Dimensions of Level-1 Group-Based Phylogenetic Net…

In a recursive way and by including a parameter, we introduce a family of deterministic scale-free networks. The resulting networks exhibit small-world effects. We calculate the exact results for the degree exponent, the clustering…

We propose a geometric growth model for weighted scale-free networks, which is controlled by two tunable parameters. We derive exactly the main characteristics of the networks, which are partially determined by the parameters. Analytical…

Phylogenetic networks provide a more general description of evolutionary relationships than rooted phylogenetic trees. One way to produce a phylogenetic network is to randomly place $k$ arcs between the edges of a rooted binary phylogenetic…

Less rigid than phylogenetic trees, phylogenetic networks allow the description of a wider range of evolutionary events. In this note, we explain how to extend the rank invariants from phylogenetic trees to phylogenetic networks evolving…

We extend the standard scale-free network model to include a ``triad formation step''. We analyze the geometric properties of networks generated by this algorithm both analytically and by numerical calculations, and find that our model…

Recently, so-called treebased phylogenetic networks have gained considerable interest in the literature, where a treebased network is a network that can be constructed from a phylogenetic tree, called the base tree, by adding additional…

A scale-free network is grown in the Euclidean space with a global directional bias. On a vertical plane, nodes are introduced at unit rate at randomly selected points and a node is allowed to be connected only to the subset of nodes which…

We introduce a simple one-parameter network growth algorithm which is able to reproduce a wide variety of realistic network structures but without having to invoke any global information about node degrees such as preferential-attachment…

This paper establishes a relation between scale-free networks and Markov chains, and proposes a computation framework for degree distributions of scale-free networks. We first find that, under the BA model, the degree evolution of…

In phylogenetics, tree-based networks are used to model and visualize the evolutionary history of species where reticulate events such as horizontal gene transfer have occurred. Formally, a tree-based network $N$ consists of a phylogenetic…

It is well-known that the space of derivations of $n$-dimensional evolution algebras with non-singular matrices is zero. On the other hand, the space of derivations of evolution algebras with matrices of rank $n-1$ has also been completely…

Phylogenetic networks are a generalization of phylogenetic trees that are used in biology to represent reticulate or non-treelike evolution. Recently, several algorithms have been developed which aim to construct phylogenetic networks from…

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…

Simple stochastic models for phylogenetic trees on species have been well studied. But much paleontology data concerns time series or trees on higher-order taxa, and any broad picture of relationships between extant groups requires use of…

We introduce a stochastic model of growing networks where both, the number of new nodes which joins the network and the number of connections, vary stochastically. We provide an exact mapping between this model and zero range process, and…

We present a general class of geometric network growth mechanisms by homogeneous attachment in which the links created at a given time $t$ are distributed homogeneously between a new node and the exising nodes selected uniformly. This is…

Inference of phylogenetic networks is of increasing interest in the genomic era. However, the extent to which phylogenetic networks are identifiable from various types of data remains poorly understood, despite its crucial role in…

Motivated by a recently introduced network growth mechanism that rely on the ranking of node prestige measures [S. Fortunato \emph{et al}., Phys. Rev. Lett. \textbf{96}, 218701 (2006)], a rank-based model for weighted network evolution is…

We introduce a Markov model for the evolution of a gene family along a phylogeny. The model includes parameters for the rates of horizontal gene transfer, gene duplication, and gene loss, in addition to branch lengths in the phylogeny. The…

Evolutionary relationships between species are represented by phylogenetic trees, but these relationships are subject to uncertainty due to the random nature of evolution. A geometry for the space of phylogenetic trees is necessary in order…