相关论文: Combinatorial Topological Models for Phylogenetic …

Phylogenetic networks generalize phylogenetic trees, and have been introduced in order to describe evolution in the case of transfer of genetic material between coexisting species. There are many classes of phylogenetic networks, which can…

The supertree problem asking for a tree displaying a set of consistent input trees has been largely considered for the reconstruction of species trees. Here, we rather explore this framework for the sake of reconstructing a gene tree from a…

Choi et. al (2011) introduced a minimum spanning tree (MST)-based method called CLGrouping, for constructing tree-structured probabilistic graphical models, a statistical framework that is commonly used for inferring phylogenetic trees.…

Merge trees are a valuable tool in the scientific visualization of scalar fields; however, current methods for merge tree comparisons are computationally expensive, primarily due to the exhaustive matching between tree nodes. To address…

Recently much attention has been devoted to the construction of phylogenetic networks which generalize phylogenetic trees in order to accommodate complex evolutionary processes. Here we present an efficient, practical algorithm for…

Phylogenetic trees and networks are graphs used to model evolutionary relationships, with trees representing strictly branching histories and networks allowing for events in which lineages merge, called reticulation events. While the…

We introduce new methods for phylogenetic tree quartet construction by using machine learning to optimize the power of phylogenetic invariants. Phylogenetic invariants are polynomials in the joint probabilities which vanish under a model of…

The ancestral maximum-likelihood and phylogeography problems are two fundamental problems involving evolutionary studies. The ancestral maximum-likelihood problem involves identifying a rooted tree alongside internal node sequences that…

Phylogenetic networks are a generalization of phylogenetic trees allowing for the representation of non-treelike evolutionary events such as hybridization. Typically, such networks have been analyzed based on their `level', i.e. based on…

We present a new approach, the Topograph, which reconstructs underlying physics processes, including the intermediary particles, by leveraging underlying priors from the nature of particle physics decays and the flexibility of message…

Many popular algorithms for searching the space of leaf-labelled trees are based on tree rearrangement operations. Under any such operation, the problem is reduced to searching a graph where vertices are trees and (undirected) edges are…

Suppose N is a phylogenetic network indicating a complicated relationship among individuals and taxa. Often of interest is a much simpler network, for example, a species tree T, that summarizes the most fundamental relationships. The…

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…

A technique named Feature Learning from Image Markers (FLIM) was recently proposed to estimate convolutional filters, with no backpropagation, from strokes drawn by a user on very few images (e.g., 1-3) per class, and demonstrated for…

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…

We consider the NP-hard Tree Containment problem that has important applications in phylogenetics. The problem asks if a given leaf-labeled network contains a subdivision of a given leaf-labeled tree. We develop a fast algorithm for the…

Phylogenetic networks allow modeling reticulate evolution, capturing events such as hybridization and horizontal gene transfer. A fundamental computational problem in this context is the Tree Containment problem, which asks whether a given…

Phylogenetic networks are generalizations of phylogenetic trees that allow the representation of reticulation events such as horizontal gene transfer or hybridization, and can also represent uncertainty in inference. A subclass of these,…

Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…

The construction of a dendogram on a set of individuals is a key component of a genomewide association study. However even with modern sequencing technologies the distances on the individuals required for the construction of such a…