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
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.
Topics & Concepts
Genetic diversityPhylogenetic treePhylogeneticsEvolutionary biologyDiversity (politics)Distribution (mathematics)GenomeBiologyComputational biologyGeneticsMathematicsGeneMedicinePopulationMathematical analysisAnthropologyEnvironmental healthSociologyGenomics and Phylogenetic StudiesHerpesvirus Infections and TreatmentsHIV Research and Treatment