A critical assessment of gene catalogs for metagenomic analysis

Paper assessing gene catalogs for metagenomic analysis published

BEAGLE Software

A general purpose library for evaluating the likelihood of sequence evolution on trees

High-Performance Computing for Statistical Phylogenetics

Statistical phylogenetic analyses based on maximum likelihood (ML) and Bayesian inference are computationally challenging because of the intensive nature of the calculations required. At the core of statistical phylogenetics is the calculation of the likelihood (probability) of the observed molecular sequence character states under a specific model of evolution using a recursive algorithm, and the computation of this calculation comprises most of the running time for analyses. Decreasing the time (wall clock) for this computation is the raison d’être for the BEAGLE library, a parallel computing platform for high-performance calculation of phylogenetic likelihoods that makes efficient use of the fine-scale parallelization capabilities of computer processors, especially graphics processing units (GPUs).

National Science Foundation award to increase performance of BEAGLE library for SARS-CoV-2 genomic data

Cummings Receives NSF Funding to Improve Analyses of COVID-19 Genomic Data

BEAGLE 3: improved performance, scaling, and usability for a high-performance computing library for statistical phylogenetics

Paper describing BEAGLE library version 3 published

Rerooting trees increases opportunities for concurrent computation and results in markedly improved performance for phylogenetic inference

Paper describing increased performance from rerooting trees published

BEAGLE project wins NVIDIA Global Impact Award

UMD Computational Biologists Win NVIDIA Global Impact Award