Fig. 4.

Recovered clonal structure improves inference of selection in simulated data. Performance of five methods for inference of a) integrated allele frequency covariance, b) selection coefficients, and c) haplotype fitness. The left column shows rank correlations with true values, and the right column shows the mean absolute error (MAE) of inferred values versus true values. The True method uses the true allele frequency covariance matrix, which is not available in short-read data, and represents the ideal performance.