Related papers: A Corrected Parsimony Criterion for Reconstructing…

Motivation: Word-based or `alignment-free' methods for phylogeny reconstruction are much faster than traditional approaches, but they are generally less accurate. Most of these methods calculate pairwise distances for a set of input…

We consider the problem of inferring an ancestral state from observations at the leaves of a tree, assuming the state evolves along the tree according to a two-state symmetric Markov process. We establish a general branching rate condition…

The data preprocessing stage is crucial in clustering. Features may describe entities using different scales. To rectify this, one usually applies feature normalisation aiming at rescaling features so that none of them overpowers the others…

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…

In this paper we review some recent results that shed light on a fundamental question in molecular systematics: how much phylogenetic `signal' can we expect from characters that have evolved under some Markov process? There are many sides…

Gene tree/species tree reconciliation is a recent decisive progress in phylo-genetic methods, accounting for the possible differences between gene histories and species histories. Reconciliation consists in explaining these differences by…

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…

In many applications of evolutionary algorithms the computational cost of applying operators and storing populations is comparable to the cost of fitness evaluation. Furthermore, by knowing what exactly has changed in an individual by an…

In many interesting cases the reconstruction of a correct phylogeny is blurred by high mutation rates and/or horizontal transfer events. As a consequence a divergence arises between the true evolutionary distances and the differences…

Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…

In this paper we provide a novel mathematical optimization based methodology to perturb the features of a given observation to be re-classified, by a tree ensemble classification rule, to a certain desired class. The method is based on…

Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…

It is common in phylogenetics to have some, perhaps partial, information about the overall evolutionary tree of a group of organisms and wish to find an evolutionary tree of a specific gene for those organisms. There may not be enough…

Multivariate clustering in astrophysics is a recent development justified by the bigger and bigger surveys of the sky. The phylogenetic approach is probably the most unexpected technique that has appeared for the unsupervised classification…

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 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…

Bayesian approaches to reconstructing the evolutionary history of languages rely on the tree model, which assumes that these languages descended from a common ancestor and underwent modifications over time. However, this assumption can be…

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…

Rate variation among the sites of a molecular sequence is commonly found in applications of phylogenetic inference. Several approaches exist to account for this feature but they do not usually enable the investigator to pinpoint the sites…

Reticulate evolutionary processes result in phylogenetic histories that cannot be modeled using a tree topology. Here, we apply methods from topological data analysis to molecular sequence data with reticulations. Using a simple example, we…