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

Simone Marini; Carla Mavian; Alberto Riva; Mattia Prosperi; Marco Salemi; Brittany Rife Magalis

doi:10.1093/bioinformatics/btab725

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

Bioinformatics. 2022 Jan 12;38(3):856-860. doi: 10.1093/bioinformatics/btab725.

Authors

Simone Marini^{1

2}, Carla Mavian^{2

3}, Alberto Riva⁴, Mattia Prosperi¹, Marco Salemi^{2

3}, Brittany Rife Magalis^{2

3}

Affiliations

¹ Department of Epidemiology, University of Florida, Gainesville, FL 32611, USA.
² Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA.
³ Department of Pathology, University of Florida, Gainesville, FL 32611, USA.
⁴ Bioinformatics Core, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA.

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.

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

Authors

Affiliations

Abstract

Publication types

MeSH terms

Grants and funding