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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…
Statistical consistency in phylogenetics has traditionally referred to the accuracy of estimating phylogenetic parameters for a fixed number of species as we increase the number of characters. However, as sequences are often of fixed length…
Horizontal gene transfer inference approaches are usually based on gene sequences: parametric methods search for patterns that deviate from a particular genomic signature, while phylogenetic methods use sequences to reconstruct the gene and…
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,…
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.…
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…
The goal of this paper is to study the similarity between sequences using a distance between the \emph{context} trees associated to the sequences. These trees are defined in the framework of \emph{Sparse Probabilistic Suffix Trees} (SPST),…
Phylogenetic comparative methods explore the relationships between quantitative traits adjusting for shared evolutionary history. This adjustment often occurs through a Brownian diffusion process along the branches of the phylogeny that…
Deciding whether there is a single tree -a supertree- that summarizes the evolutionary information in a collection of unrooted trees is a fundamental problem in phylogenetics. We consider two versions of this question: agreement and…
Phylogeny is the study of the relations between biological entities. From it, the need to compare tree-like graphs has risen and several metrics were established and researched, but since there is no definitive way to compare them, its…
The fairness characteristic is a critical attribute of trusted AI systems. A plethora of research has proposed diverse methods for individual fairness testing. However, they are suffering from three major limitations, i.e., low efficiency,…
This paper describes the software implementation of genetic algorithm for identifying and selecting most relevant results received during sequentially executed subject search operations. Simulated evolutionary process generates sustainable…
Plant phenotyping refers to a quantitative description of the plants properties, however in image-based phenotyping analysis, our focus is primarily on the plants anatomical, ontogenetical and physiological properties.This technique…
The inference of phylogenetic networks, which model complex evolutionary processes including hybridization and gene flow, remains a central challenge in evolutionary biology. Until now, statistically consistent inference methods have been…
Inference of network-like evolutionary relationships between species from genomic data must address the interwoven signals from both gene flow and incomplete lineage sorting. The heavy computational demands of standard approaches to this…
Phylogenetically decisive collections of taxon sets have the property that if trees are chosen for each of their elements, as long as these trees are compatible, the resulting supertree is unique. This means that as long as the trees…
Phylogenetic inference aims to reconstruct the evolutionary relationships of different species based on genetic (or other) data. Discrete characters are a particular type of data, which contain information on how the species should be…
Most Graph Neural Networks (GNNs) cannot distinguish some graphs or indeed some pairs of nodes within a graph. This makes it impossible to solve certain classification tasks. However, adding additional node features to these models can…
When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because…
We study the problem of similarity detection by sequence alignment with gaps, using a recently established theoretical framework based on the morphology of alignment paths. Alignments of sequences without mutual correlations are found to…