Extended Data Fig. 4: Comparison of relative likelihood scores of trees inferred by different phylogenetic methods from SARS-CoV-2 genomes.

MAPLE leads to more accurate tree reconstruction (tree topologies with higher likelihoods) both in real data and simulations. On the Y axis we show the relative log-likelihood scores (computed with IQ-TREE 2) of the tree estimated by each method, as in Fig. 4f, with higher scores representing more likely tree estimates. 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. Other details are the same as in Extended Data Figure S1.