Related papers: FrackyFrac: A Standalone UniFrac Calculator
Both the weighted and unweighted Unifrac distances have been very successfully employed to assess if two communities differ, but do not give any information about how two communities differ. We take advantage of recent observations that the…
Using modern technology, it is now common to survey microbial communities by sequencing DNA or RNA extracted in bulk from a given environment. Comparative methods are needed that indicate the extent to which two communities differ given…
UniFrac is a commonly used metric in microbiome research for comparing microbiome profiles to one another ("beta diversity"). The recently implemented Striped UniFrac added the capability to split the problem into many independent…
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.…
The advent of hardware ray tracing (RT) units has brought unprecedented realism to real-time rendered computer graphics. However, the potential of these units extends beyond graphics, offering acceleration for various computational tasks…
Phylogenetic trees are ubiquitous and central to biology, but most published trees are available only as visual diagrams and not in the machine-readable newick format. There are thus thousands of published trees in the scientific literature…
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…
Important data mining problems such as nearest-neighbor search and clustering admit theoretical guarantees when restricted to objects embedded in a metric space. Graphs are ubiquitous, and clustering and classification over graphs arise in…
Evolutionary relationships between species are usually inferred through phylogenetic analysis, which provides phylogenetic trees computed from allelic profiles built by sequencing specific regions of the sequences and abstracting them to…
We present SuperTracer, a Mathematica package aimed at facilitating the functional matching procedure for generic UV models. This package automates the most tedious parts of one-loop functional matching computations. Namely, the…
Probabilistic programming frameworks are powerful tools for statistical modelling and inference. They are not immediately generalisable to phylogenetic problems due to the particular computational properties of the phylogenetic tree object.…
We present the phylogeny analysis software SICLE (Sister Clade Extractor), an easy-to-use, high- throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the…
The existence of trace links between artifacts of the software development life cycle can improve the efficiency of many activities during software development, maintenance and operations. Unfortunately, the creation and maintenance of…
Material microstructures are traditionally compared using sets of statistical measures that are incomplete, e.g., two visually distinct microstructures can have identical grain size distributions and phase fractions. While this is not a…
The freud Python package is a powerful library for analyzing simulation data. Written with modern simulation and data analysis workflows in mind, freud provides a Python interface to fast, parallelized C++ routines that run efficiently on…
Accurate crop yield prediction relies on diverse data streams, including satellite, meteorological, soil, and topographic information. However, despite rapid advances in machine learning, existing approaches remain crop- or region-specific…
Tracers provide users with useful information about program executions. In this article, we propose a ``tracer driver''. From a single tracer, it provides a powerful front-end enabling multiple dynamic analysis tools to be easily…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
Modern scientific applications are increasingly decomposable into individual functions that may be deployed across distributed and diverse cyberinfrastructure such as supercomputers, clouds, and accelerators. Such applications call for new…
The industry and academia have proposed many distributed graph processing systems. However, the existing systems are not friendly enough for users like data analysts and algorithm engineers. On the one hand, the programing models and…