Work

Optimizing viral genome subsampling by genetic diversity and temporal distribution (TARDiS) for phylogenetics

Year: 2021

Type: article

Abstract: SUMMARY: TARDiS is a novel phylogenetic tool for optimal genetic subsampling. It optimizes both genetic diversity and temporal distribution through a genetic algorithm. AVAILABILITY AND IMPLEMENTATION: TARDiS, along with example datasets and a user manual, is available at https://github.com/smarini/tardis-phylogenetics.

Source: Bioinformatics

DOI: 10.1093/bioinformatics/btab725

Authors: Simone Marini, Carla Mavian, Alberto Riva, Mattia Prosperi, Marco Salemi, Brittany Rife Magalis

Institution: University of Florida

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: National Institutes of Health, National Institute of Allergy and Infectious Diseases, National Institute of Neurological Disorders and Stroke

Awards: Forecasting trajectories of HIV transmission networks with a novel phylodynamic and deep learning framework, HIV Dynamic Modelling for Identification of Transmission Epicenters (HIV-DYNAMITE), Viral evolution in peripheral macrophages and brain during progression to AIDS