相关论文: A Fast and Scalable Method for Inferring Phylogene…

Unrooted phylogenetic networks are graphs used to represent evolutionary relationships. Accurately reconstructing such networks is of great relevance for evolutionary biology. It has recently been conjectured that all phylogenetic networks…

Tree-child networks are an important network class which are used in phylogenetics to model reticulate evolution. In a recent paper, Pons and Batle (2021) conjectured a relation between tree-child networks and certain words. In this short…

The structure of an evolving network contains information about its past. Extracting this information efficiently, however, is, in general, a difficult challenge. We formulate a fast and efficient method to estimate the most likely history…

A phylogenetic network is a graph-theoretical tool that is used by biologists to represent the evolutionary history of a collection of species. One potential way of constructing such networks is via a distance-based approach, where one is…

Recently, considerable effort has been put into developing fast algorithms to reconstruct a rooted phylogenetic network that explains two rooted phylogenetic trees and has a minimum number of hybridization vertices. With the standard…

In the study of rooted phylogenetic networks, analyzing the set of rooted phylogenetic trees that are embedded in such a network is a recurring task. From an algorithmic viewpoint, this analysis almost always requires an exhaustive search…

We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…

It is a known fact that, given two rooted binary phylogenetic trees, the concept of maximum acyclic agreement forests is sufficient to compute hybridization networks with minimum hybridization number. In this work, we demonstrate by first…

Normal networks are an important class of phylogenetic networks that have compelling mathematical properties which align with intuition about inference from genetic data. While tools enabling widespread use of phylogenetic networks in the…

We introduce a simple algorithm for reconstructing phylogenies from multiple gene trees in the presence of incomplete lineage sorting, that is, when the topology of the gene trees may differ from that of the species tree. We show that our…

The Persistent-Phylogeny Model is an extension of the widely studied Perfect-Phylogeny Model, encompassing a broader range of evolutionary phenomena. Biological and algorithmic questions concerning persistent phylogeny have been intensely…

Networks are ubiquitous in biology and computational approaches have been largely investigated for their inference. In particular, supervised machine learning methods can be used to complete a partially known network by integrating various…

'Tree-based' phylogenetic networks proposed by Francis and Steel have attracted much attention of theoretical biologists in the last few years. At the heart of the definitions of tree-based phylogenetic networks is the notion of 'support…

Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…

Orthologous genes, which arise through speciation, play a key role in comparative genomics and functional inference. In particular, graph-based methods allow for the inference of orthology estimates without prior knowledge of the underlying…

A normal network is uniquely determined by the set of phylogenetic trees that it displays. Given a set $\mathcal{P}$ of rooted binary phylogenetic trees, this paper presents a polynomial-time algorithm that reconstructs the unique binary…

Phylogenetic networks are used to represent the evolutionary history of species. Recently, the new class of orchard networks was introduced, which were later shown to be interpretable as trees with additional horizontal arcs. This makes the…

Least squares estimation of phylogenies is an established family of methods with good statistical properties. State-of-the-art least squares phylogenetic estimation proceeds by first estimating a distance matrix, which is then used to…

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,…

We present an efficient phylogenetic reconstruction algorithm allowing insertions and deletions which provably achieves a sequence-length requirement (or sample complexity) growing polynomially in the number of taxa. Our algorithm is…