Related papers: Fast phylogeny reconstruction through learning of …
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
In evolutionary biology, genetic sequences carry with them a trace of the underlying tree that describes their evolution from a common ancestral sequence. The question of how many sequence sites are required to recover this evolutionary…
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…
We present an algorithm for phylogenetic reconstruction using quartets that returns the correct topology for $n$ taxa in $O(n \log n)$ time with high probability, in a probabilistic model where a quartet is not consistent with the true…
In evolutionary biology, the speciation history of living organisms is represented graphically by a phylogeny, that is, a rooted tree whose leaves correspond to current species and branchings indicate past speciation events. Phylogenies are…
Background: The reconstruction of the phylogenetic tree topology of four taxa is, still nowadays, one of the main challenges in phylogenetics. Its difficulties lie in considering not too restrictive evolutionary models, and correctly…
Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov…
We propose a reinforcement-learning algorithm to tackle the challenge of reconstructing phylogenetic trees. The search for the tree that best describes the data is algorithmically challenging, thus all current algorithms for phylogeny…
An evolutionary tree is a cascade of bifurcations starting from a single common root, generating a growing set of daughter species as time goes by. Species here is a general denomination for biological species, spoken languages or any other…
One of the goals of phylogenetic research is to find the species tree describing the evolutionary history of a set of species. But the trees derived from geneti data with the help of tree inference methods are gene trees that need not…
Phylogenetic tree inference using deep DNA sequencing is reshaping our understanding of rapidly evolving systems, such as the within-host battle between viruses and the immune system. Densely sampled phylogenetic trees can contain special…
In this paper, we study the parallel query complexity of reconstructing biological and digital phylogenetic trees from simple queries involving their nodes. This is motivated from computational biology, data protection, and computer…
We describe a method that will reconstruct an unrooted binary phylogenetic level-1 network on n taxa from the set of all quartets containing a certain fixed taxon, in O(n^3) time. We also present a more general method which can handle more…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
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…
Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed to this purpose. Theoretical results are available that show…
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…
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…
The reconstruction of phylogenies from DNA or protein sequences is a major task of computational evolutionary biology. Common phenomena, notably variations in mutation rates across genomes and incongruences between gene lineage histories,…