Related papers: Pattern-based phylogenetic distance estimation and…

Phylogenetic inference, the task of reconstructing how related sequences evolved from common ancestors, is a central objective in evolutionary genomics. The current state-of-the-art methods exploit probabilistic models of sequence evolution…

We present a new whole-genome based approach to infer large-scale phylogenies that is alignment- and reference-free. In contrast to other methods, it does not rely on pairwise comparisons to determine distances to infer edges in a tree.…

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…

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…

There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…

Inferring the phylogenetic relationships among a sample of organisms is a fundamental problem in modern biology. While distance-based hierarchical clustering algorithms achieved early success on this task, these have been supplanted by…

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…

The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…

As whole genomes become widely available, maximum likelihood and Bayesian phylogenetic methods are demonstrating their limits in meeting the escalating computational demands. Conversely, distance-based phylogenetic methods are efficient,…

Within bioinformatics, the textual alignment of amino acid sequences has long dominated the determination of similarity between proteins, with all that implies for shared structure, function and evolutionary descent. Despite the relative…

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.…

We introduce a new phylogenetic reconstruction algorithm which, unlike most previous rigorous inference techniques, does not rely on assumptions regarding the branch lengths or the depth of the tree. The algorithm returns a forest which is…

Phylogenomic approaches developed thus far are either too time-consuming or lack a solid evolutionary basis. Moreover, no phylogenomic approach is capable of constructing a tree directly from unassembled raw sequencing data. A new…

Distance-based approaches in phylogenetics such as Neighbor-Joining are a fast and popular approach for building trees. These methods take pairs of sequences from them construct a value that, in expectation, is additive under a stochastic…

Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…

Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly.…

We introduce a scale-free method for testing the proportionality of branch lengths between two phylogenetic trees that have the same topology and contain the same set of taxa. This method scales both trees to a total length of 1 and sums up…

Phylogenomics, even more so than traditional phylogenetics, needs to represent the uncertainty in evolutionary trees due to systematic error. Here we illustrate the analysis of genome-scale alignments of yeast, using robust measures of the…

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…

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…