Related papers: PhyloGen: Language Model-Enhanced Phylogenetic Inf…
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…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
The amount of completely sequenced chloroplast genomes increases rapidly every day, leading to the possibility to build large scale phylogenetic trees of plant species. Considering a subset of close plant species defined according to their…
Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed phylogenetic network, representing the evolutionary history of certain species. Tree Containment asks whether the given phylogenetic tree (for…
Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. This makes phylogenetic networks a more comprehensive…
Phylogenomics is a new field which applies to tools in phylogenetics to genome data. Due to a new technology and increasing amount of data, we face new challenges to analyze them over a space of phylogenetic trees. Because a space of…
A phylogenetic tree is an important way in Bioinformatics to find the evolutionary relationship among biological species. In this research, a proposed model is described for the estimation of a phylogenetic tree for a given set of data. To…
The typical problem in Data Science is creating a structure that encodes the occurrence frequency of unique elements in rows and relations between different rows of a data frame. We present the probability tree abstract data structure, an…
Generative models derived from large protein sequence alignments define complex fitness landscapes, but their utility for accurately modeling non-equilibrium evolutionary dynamics remains unclear. In this work, we perform a rigorous…
Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation…
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 $X$…
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…
Phylogenetic trees are the fundamental mathematical representation of evolutionary processes in biology. They are also objects of interest in pure mathematics, such as algebraic geometry and combinatorics, due to their discrete geometry.…
Phylogenetic diversity indices are commonly used to rank the elements in a collection of species or populations for conservation purposes. The derivation of these indices is typically based on some quantitative description of the…
With the astonishing rate that the genomic and metagenomic sequence data sets are accumulating, there are many reasons to constrain the data analyses. One approach to such constrained analyses is to focus on select subsets of gene families…
In evolutionary studies it is common to use phylogenetic trees to represent the evolutionary history of a set of species. However, in case the transfer of genes or other genetic information between the species or their ancestors has…
Phylogenetic mixtures model the inhomogeneous molecular evolution commonly observed in data. The performance of phylogenetic reconstruction methods where the underlying data is generated by a mixture model has stimulated considerable recent…
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…
We propose a novel method for the inference of phylogenetic trees that utilises point configurations on hyperbolic space as its optimisation landscape. Each taxon corresponds to a point of the point configuration, while the evolutionary…
Dependency trees help relation extraction models capture long-range relations between words. However, existing dependency-based models either neglect crucial information (e.g., negation) by pruning the dependency trees too aggressively, or…