相关论文: Lattice consensus: A partial order on phylogenetic…

We answer two questions raised by Bryant, Francis and Steel in their work on consensus methods in phylogenetics. Consensus methods apply to every practical instance where it is desired to aggregate a set of given phylogenetic trees (say,…

In a recent study, Bryant, Francis and Steel investigated the concept of \enquote{future-proofing} consensus methods in phylogenetics. That is, they investigated if such methods can be robust against the introduction of additional data like…

Connected acyclic graphs (trees) are data objects that hierarchically organize categories. Collections of trees arise in a diverse variety of fields, including evolutionary biology, public health, machine learning, social sciences and…

A consensus tree is a phylogenetic tree that synthesizes a given collection of phylogenetic trees, all of which share the same leaf labels but may have different topologies, typically obtained through bootstrapping. Our research focuses on…

An important and well-studied problem in phylogenetics is to compute a \emph{consensus tree} so as to summarize the common features within a collection of rooted phylogenetic trees, all whose leaf-sets are bijectively labeled by the same…

An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…

Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…

Consensus methods provide a useful strategy for combining information from a collection of gene trees. An important application of consensus methods is to combine gene trees to estimate a species tree. To investigate the theoretical…

The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data.…

Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…

A consensus tree is a phylogenetic tree that captures the similarity between a set of conflicting phylogenetic trees. The problem of computing a consensus tree is a major step in phylogenetic tree reconstruction. It also finds applications…

Metrics on rooted phylogenetic trees are integral to a number of areas of phylogenetic analysis. Cluster-similarity metrics have recently been introduced in order to limit skew in the distribution of distances, and to ensure that trees in…

Consensus methods are widely used for combining phylogenetic trees into a single estimate of the evolutionary tree for a group of species. As more taxa are added, the new source trees may begin to tell a different evolutionary story when…

Phylogenetic networks are a generalization of evolutionary or phylogenetic trees that are commonly used to represent the evolution of species which cross with one another. A special type of phylogenetic network is an {\em $X$-cactus}, which…

In phylogenetics, the consensus problem consists in summarizing a set of phylogenetic trees that all classify the same set of species into a single tree. Several definitions of consensus exist in the literature; in this paper we focus on…

The standard approach to estimate species trees is to align a selected set of genes, concatenate the alignments and then estimate a consensus tree. However, individual genes contain differing levels of evolutionary information, either…

We introduce a notion of finite sampling consistency for phylogenetic trees and show that the set of finitely sampling consistent and exchangeable distributions on n leaf phylogenetic trees is a polytope. We use this polytope to show that…

The evolutionary relationships between species are typically represented in the biological literature by rooted phylogenetic trees. However, a tree fails to capture ancestral reticulate processes, such as the formation of hybrid species or…

Bayesian inference is now a leading technique for reconstructing phylogenetic trees from aligned sequence data. In this short note, we formally show that the maximum posterior tree topology provides a statistically consistent estimate of a…

Phylogenetic trees are leaf-labelled trees used to model the evolution of species. In practice it is not uncommon to obtain two topologically distinct trees for the same set of species, and this motivates the use of distance measures to…