Related papers: A Perl Package and an Alignment Tool for Phylogene…
The displayed tree phylogenetic network model is shown to sit as a natural submodel of the graphical model associated to a directed acyclic graph (DAG). This representation allows to derive a number of results about the displayed tree…
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…
Most of the problems in genetic algorithms are very complex and demand a large amount of resources that current technology can not offer. Our purpose was to develop a Java-JINI distributed library that implements Genetic Algorithms with…
Tree alignment graphs (TAGs) provide an intuitive data structure for storing phylogenetic trees that exhibits the relationships of the individual input trees and can potentially account for nested taxonomic relationships. This paper…
A phylogeny describes the evolutionary history of an evolving population. Evolutionary search algorithms can perfectly track the ancestry of candidate solutions, illuminating a population's trajectory through the search space. However,…
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…
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…
We present JDLL, an agile Java library that offers a comprehensive toolset/API to unify the development of high-end applications of DL for bioimage analysis and to streamline their installation and maintenance. JDLL provides all the…
Biological tree (BioTree) analysis is a foundational tool in biology, enabling the exploration of evolutionary and differentiation relationships among organisms, genes, and cells. Traditional tree construction methods, while instrumental in…
Phylogenetic networks are an important way to represent evolutionary histories that involve reticulations such as hybridization or horizontal gene transfer, yet fundamental questions such as how many networks there are that satisfy certain…
Phylogenetics begins with reconstructing biological family trees from genetic data. Since Nature is not limited to tree-like histories, we use networks to organize our data, and have discovered new polytopes, metric spaces, and simplicial…
Identifying and understanding the large-scale biodiversity patterns in time and space is vital for conservation and addressing fundamental ecological and evolutionary questions. Network-based methods have proven useful for simplifying and…
GraphNeuralNetworks.jl is an open-source framework for deep learning on graphs, written in the Julia programming language. It supports multiple GPU backends, generic sparse or dense graph representations, and offers convenient interfaces…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterised by an instantaneous rate…
High-throughput pheno-, geno-, and envirotyping allows characterization of plant genotypes and the trials they are evaluated in, producing different types of data. These different data modalities can be integrated into statistical or…
Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…
Collapse Lineage Tree (CLTree) is a software tool that annotates, roots, and evaluates phylogenetic trees by using lineages. A recursive algorithm was designed to annotate the branches by the common taxonomic lineage of its descendants in a…
Phylogenetic networks are used to represent the evolutionary history of species. Recently, the new class of orchard networks was introduced, which were later shown to be interpretable as trees with additional horizontal arcs. This makes the…
In the past decade, transcriptome data have become an important component of many phylogenetic studies. Phylogenetic studies now regularly include genes from newly sequenced transcriptomes, as well as publicly available transcriptomes and…
We have developed a unified format for phylogenetic placements, that is, mappings of environmental sequence data (e.g. short reads) into a phylogenetic tree. We are motivated to do so by the growing number of tools for computing and…