Extended Data Fig. 1: Comparison of running times of all considered methods and options for phylogenetic inference from SARS-CoV-2 genomes.

Comparison of running times of all considered methods and options for phylogenetic inference from SARS-CoV-2 genomes. On the Y axis on a logarithmic scale, we show the number of seconds it takes to run each method. On the X axis is the number of sequences in the dataset considered on a logarithmic scale. Different line styles and colors represent different options for each method, as denoted in the legend and Supplementary Methods Section S1.11. We ran each method and set of options up to the maximum dataset size that was achievable due to time and memory limitations. Violin plots summarize values for 10 replicates, and dots represent their mean. A Results for subsamples from the real SARS-CoV-2 dataset. B Simulated datasets with no rate variation or ambiguity. C Results on simulated data with rate variation but no ambiguities. D Simulated data with sequence ambiguities but no rate variation.