Online Phylogenetics with matOptimize Produces Equivalent Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Implementations.

Phylogenetics has been foundational to SARS-CoV-2 research and public health policy, assisting in genomic surveillance, contact tracing, and assessing emergence and spread of new variants. However, phylogenetic analyses of SARS-CoV-2 have often relied on tools designed for de novo phylogenetic inference, in which all data are collected before any analysis is performed and the phylogeny is inferred once from scratch. SARS-CoV-2 data sets do not fit this mold.

Treenome Browser: co-visualization of enormous phylogenies and millions of genomes.

Summary: Treenome Browser is a web browser tool to interactively visualize millions of genomes alongside huge phylogenetic trees.

Availability And Implementation: Treenome Browser for SARS-CoV-2 can be accessed at cov2tree.org, or at taxonium.