Related papers: Developing and applying heterogeneous phylogenetic…
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…
Since the advent of modern bioinformatics, the challenging, multifaceted problem of reconstructing phylogenetic history from biological sequences has hatched perennial statistical and algorithmic innovation. Studies of the phylogenetic…
This paper introduces a procedure based on genetic programming to evolve XSLT programs (usually called stylesheets or logicsheets). XSLT is a general purpose, document-oriented functional language, generally used to transform XML documents…
Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov…
In the global challenge of understanding and characterizing biodiversity, short species-specific genomic sequences known as DNA barcodes play a critical role, enabling fine-grained comparisons among organisms within the same kingdom of…
This paper introduces a procedure based on genetic programming to evolve XSLT programs (usually called stylesheets or logicsheets). XSLT is a general purpose, document-oriented functional language, generally used to transform XML documents…
The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
Biological phenotypes are products of complex evolutionary processes in which selective forces influence multiple biological trait measurements in unknown ways. Phylogenetic factor analysis disentangles these relationships across the…
The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies,…
Mathematical models allow us to gain a deeper understanding of real-world dynamical systems. One of the most powerful mathematical frameworks for modeling real-world phenomena are systems of differential equations. In the majority of fields…
Computer simulations are an important tool for studying the mechanics of biological evolution. In particular, in silico work with agent-based models provides an opportunity to collect high-quality records of ancestry relationships among…
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…
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…
Evolutionary Computation is a group of biologically inspired algorithms used to solve complex optimisation problems. It can be split into Evolutionary Algorithms, which take inspiration from genetic inheritance, and Swarm Intelligence…
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…
We propose a model of the evolution of a matrix along a phylogenetic tree, in which transformations affect either entire rows or columns of the matrix. This represents the change of both lexical and phonological aspects of linguistic data,…
PhyloFrame is a Python library for phylogenetic computation targeting the gap between specialist, compiler-optimized operations and flexible, script-based workflows -- with emphasis on fast, memory-efficient operations for very large tree…
In this work, we propose the novel Prototypical Graph Regression Self-explainable Trees (ProGReST) model, which combines prototype learning, soft decision trees, and Graph Neural Networks. In contrast to other works, our model can be used…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary events acting at the population level, like recombination between genes, hybridization between lineages, and lateral gene…