Phylogenetic Tool Developed for Massive Pandemic Sequence Datasets

In Nature Genetics, researchers at the European Bioinformatics Institute's European Molecular Biology Laboratory, the Max Planck Institute for Molecular Genetics, and other centers in the US and Australia describe their "maximum parsimonious likelihood estimation" (MAPLE) approach for quickly and efficiently putting together SARS-CoV-2  phylogenies based on millions of viral genomes. The approach uses relatively little memory compared to conventional approaches that have not been developed to deal with data on the same scale. "MAPLE infers SARS-CoV-2 phylogenies more accurately than existing maximum likelihood approaches while running up to thousands of times faster, and requiring at least 100 times less memory on large datasets," the authors explain. "This extends the reach of genomic epidemiology, allowing the continued use of accurate phylogenetic, phylogeographic, and phylodynamic analyses on datasets of millions of genomes."