Related papers: Constructing a Consensus Phylogeny from a Leaf-Rem…
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…
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…
Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains…
Phylogenetic trees summarize evolutionary relationships between organisms, and tools to analyze collections of phylogenetic trees enable contrasts between different genes' ancestry. The BHV metric space has enabled the analysis of…
Historical linguistics aims at inferring the most likely language phylogenetic tree starting from information concerning the evolutionary relatedness of languages. The available information are typically lists of homologous (lexical,…
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…
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…
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…
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…
Supertree methods are tree reconstruction techniques that combine several smaller gene trees (possibly on different sets of species) to build a larger species tree. The question of interest is whether the reconstructed supertree converges…
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…
We consider a natural variant of the well-known Feedback Vertex Set problem, namely the problem of deleting a small subset of vertices or edges to a full binary tree. This version of the problem is motivated by real-world scenarios that are…
Phylogenetic trees describe the evolutionary history of a group of present-day species from a common ancestor. These trees are typically reconstructed from aligned DNA sequence data. In this paper we analytically address the following…
We consider the problem of estimating species trees from unrooted gene tree topologies in the presence of incomplete lineage sorting, a common phenomenon that creates gene tree heterogeneity in multilocus datasets. One popular class of…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new…
The Maximum Agreement Forest (Maf) problem is a well-studied problem in evolutionary biology, which asks for a largest common subforest of a given collection of phylogenetic trees with identical leaf label-set. However, the previous work…
A method for creating a forest of model trees to fit samples of a function defined on images is described in several steps: down-sampling the images, determining a tree's hyperplanes, applying convolutions to the hyperplanes to handle small…
We consider the numerical taxonomy problem of fitting a positive distance function ${D:{S\choose 2}\rightarrow \mathbb R_{>0}}$ by a tree metric. We want a tree $T$ with positive edge weights and including $S$ among the vertices so that…
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the…