Related papers: DendroPy 5: a mature Python library for phylogenet…

This paper introduces PyGAD, an open-source easy-to-use Python library for building the genetic algorithm. PyGAD supports a wide range of parameters to give the user control over everything in its life cycle. This includes, but is not…

Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…

DNA sequence analysis is fundamental to life science research. The rapid development of next generation sequencing (NGS) technologies, and the richness and diversity of applications it makes feasible, have created an enormous gulf between…

This paper introduces PhyloLM, a method adapting phylogenetic algorithms to Large Language Models (LLMs) to explore whether and how they relate to each other and to predict their performance characteristics. Our method calculates a…

Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…

For over two decades, image-based profiling has revolutionized cell phenotype analysis. Image-based profiling processes rich, high-throughput, microscopy data into thousands of unbiased measurements that reveal phenotypic patterns powerful…

Integrated information theory provides a mathematical framework to fully characterize the cause-effect structure of a physical system. Here, we introduce PyPhi, a Python software package that implements this framework for causal analysis…

We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps…

Biomedical research centers can empower basic discovery and novel therapeutic strategies by leveraging their large-scale datasets from experiments and patients. This data, together with new technologies to create and analyze it, has ushered…

Software libraries are the elementary building blocks of open source software ecosystems, extending the capabilities of programming languages beyond their standard libraries. Although ecosystem health is often quantified using data on…

Lifemapper (http://www.lifemapper.org) is a predictive electronic atlas of the Earth's biological biodiversity. Using a screensaver version of the GARP genetic algorithm for modeling species distributions, Lifemapper harnesses vast…

Deep learning has enabled major advances in the fields of computer vision, natural language processing, and multimedia among many others. Developing a deep learning system is arduous and complex, as it involves constructing neural network…

The reproducibility of scientific research has become a point of critical concern. We argue that openness and transparency are critical for reproducibility, and we outline an ecosystem for open and transparent science that has emerged…

The Astropy Project supports and fosters the development of open-source and openly-developed Python packages that provide commonly needed functionality to the astronomical community. A key element of the Astropy Project is the core package…

Data is the most powerful decision-making tool at our disposal. However, despite the exponentially growing volumes of data generated in the world, putting it to effective use still presents many challenges. Relevant data seems to be never…

In this paper, we present WildlifeDatasets (https://github.com/WildlifeDatasets/wildlife-datasets) - an open-source toolkit intended primarily for ecologists and computer-vision / machine-learning researchers. The WildlifeDatasets is…

Ancestry and genealogy tree are proven tools to determine the lineage of any person and establish dependencies among individuals. Genealogy tree can be exploited further to gain information about the researcher and his scholastic lineage…

Bibliometric analysis is a critical tool for understanding the structure, dynamics, and impact of scientific research. Traditional methods often fall short in capturing the intricate relationships and evolving trends within scientific…

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…

Archaeological pottery documentation and study represents a crucial but time-consuming aspect of archaeology. While recent years have seen advances in digital documentation methods, vast amounts of legacy data remain locked in traditional…